Effects Of Kratom Tea

Mitragynina speciosa or Kratom leaves with powder product in white ceramic bowl and water from the extracts the kratom leaves. Supplement kratom green capsules.

Borneo Kratom Tea

Our bodies operate like machines 24 hours a day to keep us healthy and functioning at optimal levels. However, despite its amazing multi-tasking abilities, sometimes it needs a boost to continue performing well. Kratom is a natural herb that has become immensely popular for its abilities to improve the workings of all bodily functions to keep it productive and healthy throughout the day and has many benefits for memory, sleep, and enhanced energy. It has opioid properties and some stimulant effects. One of the best Kratom strains available is Bali Kratom from Kratom trees native to the tropical forests of the small island of Borneo in Southeast Asia where locals have been using it as indigenous medicine for years. The leaves from this tropical, evergreen tree are rich in alkaloids, providing the best Kratom strains available in the world. As a healing agent, it has pain-relieving, anti-inflammatory, and stress reduction effects.

Types of Bali Kratom

There are three types of Kratom trees in Bali, categorized by the color of their leaf venation into red, white, and green vein types, each having different effects.

• Red Vein Bali Kratom has powerful analgesic properties with effects that last from 4 to 6 hours. It calms the nerves and induces sleep. It is most popular for sleep regulation, sedation, and pain relief. It is best taken at night or late afternoon so as not to interfere with work routines.

• White Vein Bali Kratom provides an energy boost and has stimulating effects. It produces mild euphoria and provides a moderate energy boost. It is a relaxing, moderate pain reliever that can be used at any time during the day.

• Green Borneo Kratom is most popular for its intense pain-relieving and anti-anxiety effects. The long-lasting effects are not excessively sedating which means it can be used daily to assist the body in difficult times.

Bali Kratom Powder

Dried leaves of Bali Kratom are crushed into a powder form and is one of the most versatile ways to consume Kratom. It comes in capsule form or the powder can be swallowed dry with water. It can also be added to food or drinks such as juices, milk, yogurt, smoothies, protein shakes or made into a tea.

Bali Kratom Tea

The dried powder from the Borneo leaves is ideal for making a tea that provides both energizing and relaxing effects. Many people prefer this method of taking Kratom as it has faster results. Simply add the correct dosage you wish to consume to boiling water, simmer for about ten minutes, strain and drink it hot or cold.


One to two grams of dried Kratom leaves added to 500ml of water will make two cups of tea.
As with all Kratom, lower doses tend to be more energizing while higher doses provide better pain relief. New users should start with small dosages of 0.5 – 1.0 grams. Depending on the severity of your condition you can increase the dosage taking into consideration factors such as your age and health to get the right dosage.

Living with constant pain can affect your quality of life. Prescription medication comes with serious side effects while Borneo Kratom is a natural herb that is extremely effective for the relief of acute and chronic pain. Anyone suffering from stress, anxiety, sleep irregularities, low confidence, depression, and social isolation can try Borneo Kratom. It has also been successfully used to combat withdrawal symptoms from drugs and certain medications

Rehab For Married Couples

Rehab For Married Couples

Being in a relationship is hard, but that is further compounded when both parties at the marriage are battling addiction. If you’re entirely committed to the relationship and remaining on the path to recover, here is some info you will find to be quite helpful.

Inpatient Or Outpatient

The first step you will need to determine is whether an inpatient or outpatient facility will supply you with the maximum benefit. Remember that both parties don’t need to consent to the same therapy type; it will largely depend on their individual needs.

In addition, there are sometimes occasions where a single individual is currently in healing or not a user whatsoever and another is currently using. In that case, the person who is sober may benefit more from being viewed as an outpatient while an inpatient facility can assist another person work on a good recovery plan.

Regardless of that treatment type is preferred, individuals who attend couples rehabilitation are more likely to keep sobriety than individuals who are working hard to do well while their spouse is on another path. This is because it will help deal with the alcohol and/or drug issues while also helping the few know better ways to deal with relationship stress which don’t involve taking any kind of substances.

Treatment Techniques

There are many treatment rehab for married couples available. Listed below are just three of the most common:

Behavioral Couples Therapy

This is a form of therapy that’s based on the notion of altering behavior. It typically involved setting daily treatment targets and supplying a contract for your spouse that details the aim to get rid of substance usage. The partner is supposed to offer as much support as possible in this time. It may be a bit tricky, particularly if the individual is missing in the throes of addiction, but it may be useful in many cases.

Generally, there are counseling sessions weekly where goals and progress are always discussed. This is sometimes done in individual sessions as well as in group sessions with other couples who focus on substance abuse problems too.

Medication Therapy

Many individuals have a tough time with healing since they cannot handle the symptoms of withdrawal. It is not always easy to make the choice to quit with no help in the kind of medication.

Based upon the material that has been abused, there are pharmaceutical treatments that can help reduce symptoms like cravings, depression and nervousness.

A number of the medications available can help while somebody is trying to detox in addition to during the time that this period has finished. This may or not be used as an essential part of couples rehabilitation.

Weekly Meetings

Many have heard of Alcoholics Anonymous (AA) as well as Narcotics Anonymous (NA), however there’s an alternative available called Recovering Couples Anonymous (RCA), which could possibly be a better option for people who are in relationships that were affected by substance abuse. Much like all the other meetings said, RCA is based on a 12-step method of retrieval. This is an alternative for a couple who are both a situation where only one spouse is. In the case of the latter, these meetings can help the non-using partner understand what the other is going through and allow them to work toward a common aim – sobriety.

Here is a useful checklist. If any of these apply, rehab may be the best alternative:

There are cases when violence has occurred.

  • You wind up making excuses to get a spouses drug and alcohol abuse.
  • You lack the social support needed to deal with this all on your own.
  • The connection has taken a backpack to medication use.

If at least one of those seem familiar, you should seek help as soon as possible.Working toward sobriety is never a easy task, but it may be simpler with the ideal assistance. If you or your spouse are struggling with substance abuse and you need assistance, you should certainly consider one or more of the They can help salvage your relationship and save your life.

Benefits of Bali Kratom Powder

kratom powder

What kind of kratom powder kinds are there and how do they help your health? There are a whole lot of different kinds of kratom so it can be tough to know which of these to test . Here you can learn what your options are you can find kratom that will suit you.

You’re going to need to find out whether you can buy a sample pack of kratom which has a great deal of different strains you’ll be able to try out. If you would like to obtain a sample pack, ensure you select a number of distinct strains you haven’t tried before. When you get a sample, then you’re going to need to test out every kind on its own to see whether it works great or not. You don’t wish to combine strains collectively until you are aware of what they are like so that you do not overdo it and also have a lousy experience.

White Kratom Powder Strains

These provide you more energy compared to other breeds so that you wish to make sure you’re in need of extra energy when you try this kind out. When you proceed with white strains you wish to take it slow so that you don’t get too overstimulated if you try them out. For the maximum from a white strain, it’s great to take a few grams to begin with and to work your way upward with time. Do not just go with plenty of grams at once because that will not help us to a decreased dose in many cases.

Red kratom is very good for you in the event that you would like to relax. It tends to be more like a painkiller, also, than other breeds. When you work with a red strain you may have to take a bit more of it to get the positive effects because it can be a weaker strain generally in a great deal of instances. Nonetheless, you still should take it slow just if you get a breed that’s strong. Use this type of strain whenever you have enough time to sit and relax.

What Are The Effects Of Bali Kratom?

A green kratom strain is going to be the best of both worlds in regards to relaxation and stimulation. Generally, green strains have a lot of alkaloids in them so you’ll want to consider them should you have to have stimulation and need to unwind a little. Green breeds are normally more powerful than most so that you want to take it easy with them just like with different breeds. They’re a good beginner strain since they provide the most benefits so give this kind a try if you wish to try kratom or even when you’re experienced with that. The farms in Bali tend to grow fast compared with indo, or Borneo Kratom farms. You can get nice effects for relieving anxiety from Bali kratom. Those looking for help with insomnia will enjoy this helpful effect of leaves grown in Bali

There are all kinds of other strains you can try, like the yellow selection. When you go to explore strains that are not green, white, or red then you need to understand what the strains you’re trying are like until you take a large dose. Since firms can predict any sort of kratom any colour they want, you never know what you are going to get before you try it out. So, if you come across any kratom that is a new color, start slow and see what it’s like before you attempt your routine dose outside.

Top Rated Bali Kratom Powder Products

You want to make sure that you take it or which you only take it when it’s going to benefit you. If you do need to take it daily, then once you would like to quit taking it you’re able to taper off so you don’t need to deal with withdrawals. It is best to consider quitting as slowly as possible so you are not uncomfortable. If you wind up carrying a lot of it every day you will definitely have to deal with withdrawal problems if you quit abruptly.

It’s a fantastic idea to figure out if you’re going to use kratom powder or in the event that you’ll use capsules. If you’re likely to use a powder, then you need to acquire a scale so you can tell how much you are taking. When you would like to take kratom, attempt to start at a gram or 2 and work your way up out there. Using capsules, they usually hold half a gram depending on their dimensions. Consider the packaging for the bali kratom capsules you must learn just how much is in each one before you choose them.

Our Tour of Red Bali Kratom Farm

You now know what the strains of kratom powder are and how to buy what’s going to work for you. You might discover that kratom can be hit or miss depending on what type you buy. Be certain you use what you heard here so you can get what’s going to work for you.

“On our most recent trip to Bali my wife and I found the ultimate kratom super green. Her pulmonary doctor recommended Bali kratom for chronic pain caused by inflammation due to her disease. A local tour guide drove us to a 500 acre farm where red Bali kratom is grown naturally. We were allowed to pick our own leaves from the adult trees. Most of the natives here just chew the kratom leaf without any method. Americans need to use either Bali kratom capsules or powder mixed into flavored tea. The population of Bali has grown their income level by farming these kratom trees. No longer a dirt poor country, the discovery of mitragyna speciosa by americans, has changed the lives of these hard working kratom farmers. The leaves of this type of kratom plant must be picked by hand and the farmers are happy to show us how to notice the best quality bali kratom leaves.

Next we toured the actual extraction warehouse where the locals crush the green malay kratom leaf into fine powder for shipping overseas. The product is pressed into packaged kilograms and marked for that particular strain of kratom.” Dr. Lindsey Rosen M.D.

Is Maeng Da Stronger Than Bali Kratom?

Depending on your particular reason for taking kratom there are different effects from both products. Our review of red vein species and leaves found that:

For Opiate addiction, the correct dosage of maeng da kratom will alleviate the symptoms of withdrawal from opiates like oxycodone or percocet pain medications. For those people looking for more energy, Maeng Da is more potent than other kratom in our review. If you are looking for anxiety relief or help sleeping, then Bali is the best kratom for these ailments. For pain relief, both enhanced forms of bali kratom and maeng da extract can alleviate chronic pain issues for most users. Now, there are different strengths of white vein kratom from Bali, depending on which farm grew the trees. All kratom can be addictive, so be careful not to develop a tolerance to the extract which is the most potent form of kratom.

Best Kratom For Pain Relief

Right Kratom Dosage

Among the main active components of kratom is mitragynine, an alkaloid that’s anti inflammatory, pain reliever and has muscle relaxant effects. It may be useful to individuals with arthritis, fibromyalgia, rheumatism etc.. They market capsules that are 100% natural with no preservatives, animal products or additives. They are usually wrapped in gelatin capsules making them easy to swallow. They are a fantastic alternative to kratom powder since they’ll mask the flavor of kratom.

The kratom capsules are effective for pain relief and cannot create a mess. They are available in different package sizes; from 250grams around 1kg. Using capsules, you do not need a complex measuring instrument when shooting them. Each pill has a measured quantity of kratom and you just need to find out how many to choose to relieve your pain. They are convenient to carry hence you can relieve your pain anytime and anyplace.

Best Kratom for Pain Relief

There are lots of different kratom strains. One of them is Malaysian kratom. It’s popular because of its potency hence makes among the highly effective pain killers. It’s also used as treatment for substance abuse. Borneo kratom is grown in Borneo Island. It’s available as white strand Borneo, Red vein Borneo and Green vein Borneo. Red strand Borneo is mainly used for pain because of its powerful analgesic properties.

These kinds of Borneo kratom can be consumed as powder, capsules, extract or merely make kratom tea. It is possible to take advantage of this kratom to ease anxiety and depression, boost your body energy also cure insomnia. Kratom is. In the area, the leaves were used for recreational purposes, pain relief, cure diarrhea and boost energy while working in the farms. Kratom for pain is not simply a natural remedy for pain but will enable a user overcome opioid addiction. The chemical alkaloid profiles of these strains vary depending on the geographical region they grow in and the method of extraction. This ultimately determines the benefits associated with a particular strain.

The following strains have been identified as the most effective ones to use for pain relief.

1. Bali Kratom

Bali Kratom is a combination of Borneo and Sumatra strains and has a high molecular content of the pain relieving alkaloid 7-hydroxymitragynine. It is a potent strain that users have found delivers both chronic pain relief and a stimulating energy boost. It is available in all three vein colors – red, green, and white strains.

The #1 most potent Kratom strain we have found for pain is this Red Bali strain which has totally taken away pain for 3-7 hours continuously in our surveyed patient experience.

For chronic pain relief, the Bali Red vein is the best choice. In addition to being highly potent, it’s fast acting and effects can last between 3-7 hours. It does also have a strong sedating effect so is best taken prior to going to sleep. Users also report that wobbles are common when using this strain. These can be avoided consuming medium moderate doses or by blending it with another green strain.

2. Maeng Da Kratom

Maeng Da is one of the more popular Kratom options. Its uniqueness stems from the fact that it did not start out as naturally occurring variety. It is said to have been specifically bred to have higher concentrations of Mitragynine and 7-hydroxymitragynine. This combination of alkaloids makes this strain one of the stronger potency varieties currently available. Unlike Bali Kratom, this strain is more energy stimulating than sedating so can be taken during the day.

Red vein Maeng Da is the strongest, most potent of all the three vein colors available. Since this is more of an energy producing strain it can be used as a day time painkiller. Users use it for fibromyalgia, Chronic fatigue syndrome (CFS), rheumatoid arthritis, osteoarthritis, cancer symptoms or chronic lower back pain.

3. Malay Kratom

Green Malay Kratom has lower concentrations of the alkaloid mitragynine. its a good option if you are experiencing ony minor pain or inflammation. It produces strong pain relief effects but they are not as sedative as Borneo or Bali strains. It is a good option for those whose physical pain is affecting their productivity.

The go to vein color for pain relief is red or green. Green vein Malay which may also be referred to as Super Green Malay, combines analgesic effects similar to pain meds with stimulation, anxiety relief, focus and mood enhancement. Its effects are long lasting, up to 8 hours. Some people prefer to blend this strain with Red Vein Maeng Da to make it more potent.

How Does Kratom Work for Pain Management?

Pain is very common. A lot of individuals have ongoing pain that could be uncomfortable and inconvenient. You’re able to handle pain with kratom which is a natural remedy and good alternative to pharmaceutical medications which cause adverse side effects. When you find the most effective dosage of kratom for alleviating arthritis symptoms, such as inflammation in the joints or cracking knees, it works like hydrocodone or other pain medications. In our most recent survey of kratom users, we found helpful benefits reported by users of maeng da kratom, mitragyna speciosa. Those using Bali kratom repoted more sedative effects of kratom. The recent news article that reported on the use of kratom for opiate withdrawal symptoms showed university studies on addicts successful in quitting heroin.

Research Studies on Kratom

Given the current opioid crisis, kratom is being sought out and used as an alternative to pain medication. Opioid drugs like Percocet or Vicodin are very addictive and sometimes can be misused due to their high effects. Kratom is 100% safe to consume and you can not overdose on it. There are different strains of kratom that you can buy online for pain. Kratom is available on the internet in the form of leaf extracts, capsules, powder, pills etc.

Many proponents of kratom suggest that the natural herb could serve as a solution to the opioid crisis, both by offering another option for chronic pain relief and by aiding those struggling to overcome opioid addiction.

Other science experts say that it may not the magic solution some people claim it is.

Published peer reviewewd research on kratom’s possible benefits as a pain reliever and opioid alternative is very scarce. The available research includes a report published in the International Journal on Drug Policy in 2010, for which university scientists surveyed 137 active users of kratom and found that the herb was “described as affordable, easily available, and having no serious side effects despite prolonged use.” This report included no testing of kratom’s health effects or potential hazards.

In a more recent report published in Drug and Alcohol Dependence in 2014, researchers surveyed 293 regular kratom users and determined that more than half had developed severe dependence problems, including kratom withdrawal symptoms like muscle spasms, sleep disruption, anger, and tension, but relative to heroin withdrawal it is very mild

A university of Florida based study published in the Journal of Medicinal Chemistry in 2016 indicated that kratom may not slow breathing to the same extent as other pain-relieving drugs like morphine. Given that deaths due to opioid overdose are usually the result of respiratory depression, the study’s finding suggests that further peer reviewed research on the compounds in kratom is warranted.

Kratom Shown To Be Analgesic in Mice

This research study published in the ACS Central Science Journal in June 2019 issue shows, “To build on the preceding results, we hoped to examine whether 7-OH is in fact formed as a metabolite of mitragynine in vivo. Further, we sought to test whether 7-OH, as a metabolite, could be a key mediator of the analgesic effects of mitragynine. However, before proceeding with these experiments, we first set out to confirm the analgesic activity of mitragynine in our own hands and to determine whether these effects are dependent on MOR.

For this purpose, we used the 129 mouse strain, which we found to be sensitive to mitragynine-induced analgesia, consistent with the documented high sensitivity of this strain to opioid agonists. Further, genetic knockouts of opioid receptors are available on this genetic background. Dose–response curves were generated for mitragynine administered by both oral (p.o.) and subcutaneous (s.c.) routes using the tail-flick test, a classic rodent model for analgesic activity. We found that mitragynine was much more potent when administered p.o. (ED50 = 2.1 mg/kg) than when administered s.c. (ED50 = 106 mg/kg), consistent with earlier literature reports. To establish the opioid receptor dependence of these effects, an efficacious analgesic dose of mitragynine (10 mg/kg, p.o.) was administered to MOR knockout (KO), κ-opioid receptor (KOR) KO, and δ-opioid receptor (DOR) KO mice, and to wild-type (WT) mice following pretreatment with the opioid receptor antagonist naloxone (1 mg/kg, s.c.). Both MOR KO and naloxone pretreatment significantly attenuated the analgesic effect of mitragynine, whereas KOR KO and DOR KO had no effect.” Arthur Kruegel at the Department of Neuroscience, Columbia University, New York stated, “Therefore, the analgesic activity of mitragynine was found to be MOR-dependent, consistent with prior literature demonstrating pharmacological blockade of analgesia with the opioid receptor antagonist naloxoneWe have found that the opioid pharmacology of mitragynine is complicated by the important role of an active metabolite, 7-OH, in mediating its activity. This apparent requirement for metabolic activation is consistent with the higher analgesic potency of mitragynine administered orally versus parenterally in animals. Further, it suggests a possible explanation for the seemingly improved safety profile of mitragynine compared to classical opioid agonists. However, the critical involvement of hepatic metabolism also complicates our understanding of mitragynine’s pharmacology and introduces the possibility of interindividual variability in the compound’s potential therapeutic effects and side effects. We believe mitragynine and related compounds have great potential as future therapeutics, but metabolic processes must be carefully considered as the field continues to advance.”

Pain Relieving Effects Of Kratom

Kratom powder comes from kratom leaves. The leaves are dried and crushed to form powder. It is by far the most common kind of kratom. Kratom can taste horrible to a brand new user and there are plenty of ways to bypass the taste. You are able to mix the powder with your beverages in order to mask the taste. Moreover, you can measure your preferred dose, place it in mouth and wash it with almost any drink. Kratom powder can be consumed as a health supplement to improve energy and manage anxiety and depression. Pain is an unpleasant sensation linked to tissue injury. It has a significant role of preventing tissue damage within the body. It can feel as a stabbing or a dull ache. It’s either acute or chronic.

Pain can be caused by bone fractures, cuts, and burns, diseases such as arthritis, rheumatism, muscle strain, headache, stomach ache, to mention a few. You are feeling the pain when the nervous system is triggered. Chronic pain lasts 3 to 6 weeks although acute pain will disappear on its own. Living with chronic pain is challenging but you may do it. There are several approaches to treat and handle it. However, they cause undesirable side effects if used for a very long time like addiction, withdrawal symptoms, nausea, headache, etc..

How to Get Back Pain Relief Through Bali Kratom Capsules Dosage

bali kratom capsules for pain relief, kratom Pain Relief, kratom capsules for back pain

Most of the jobs today include sitting in front of the computer. Your poor posture and endless shifts at work result in intense back pain. Exercising daily helps, but do you get enough time to do that? In this fast paced world, your health problems are increasing. You compromise on health to improve your productivity.

Side-effect of Prescription Drugs

You move towards prescription drugs, thinking that they would fix your problem. Anyone who has had first hand experience with prescription drugs knows how likely they are to mess up with your system. The side-effects go from rashes to heart diseases. Their effectiveness lasts only for a short period of time.

Kratom – New Solution for Pain Relief

Kratom is a new solution for pain management. Its pain relieving qualities give you the kind of comfort you deserve. It is a herbal solution, which will assure you that it is safe. Kratom contains alkaloids that help you in getting relief. It connects with receptors that are responsible for providing back pain relief. These effects relax your body and get rid of any tightness that you would have felt otherwise.

Understand How Kratom Works

The chemistry behind Kratom is simple. Whenever you go through an injury or even a scratch, your body sends a response to the nervous system. Kratom intervenes at this process. Through its unique properties, it connects with opioid receptors for relieving your pain.

Choose Effective Kratoms

Kratom has a wide range of strains. All of these strains have unique properties which are effective for back pain relief. Almost all have some level of pain relieving properties. Choose Kraom strains that respond to your level of pain. To have a successful result, you need to select the right type of Kratom. Your Kratom vendor will help you in making the right choice to get back pain relief.

Kratom Strains That Work Best

If you struggle with managing your back pain, then these Kratom strains will solve all your problems. Back pain relief has never been this easy!

Red Bali is by far the most effective for back pain relief. It gives you sedating effects like no other strain. Use it before you sleep, because it needs some time. In terms of price, this strain is the reasonable as well. Pain relief is not an expensive option anymore.

The second is Borneo, which comes below Red Bali. Borneo has variety of veins under it. It deals best with chronic pain or any type of muscle pain.

Third comes Maeng Da. This is no doubt a very strong Kratom strain. The bali kratom capsules dosage has double benefits: it relieves your pain and also uplifts your mood like no other. If you are interested in type, then make sure you buy White Vein in Maeng Da.

You are now ready to bid farewell to your back pain. After consuming Kratom, you would not have to go through another day in pain. If you are a workaholic with back pain, this is for you!

My Software Research

Hello and welcome to my academic website. Here you can find information about my research, publications, software development, and other news. I (hope to) regularly write posts on topics related to ecology, evolution and bioinformatics with the goal of documenting fun stories and useful Python and R code. I’m currently a post-doc in the Donoghue Lab at Yale University. Before starting here I earned by Bachelors at the University of Minnesota, worked as a research associate at Brown University, and earned my PhD at the University of Chicago. 

Primary research interests:

  • Genomics: RADseq bioinformatics and phylogenetics
  • Ecology: Interspecific reproductive interference in hyperdiverse lineages
  • Evolution: Comparative approaches to measuring genomic introgression
  • Botany: Pollen-pistil relationships and floral evolution in Pedicularis
my software research


Bioinformatics – I created and still actively develop and research the program pyrad, which is used to assemble genomic RADseq data sets. I love learning about Python programming and linux, and I’m a huge advocate for open-source code and data sharing. You can follow active development of my projects on github.

Reproductive Interference – My research software is broadly focused on understanding why some clades of organisms contain more species than others, and within this context I’m especially interested in the long-recognized relationship among flowering plants where families with more specialized pollination mechanisms tend to contain more species. To understand this pattern I study how flower evolution affects rates of speciation, and reciprocally, how interactions among co-occurring species, especially within highly diverse clades, affect flower evolution.

Pedicularis – Much of my research is focused on the hyperdiverse genus Pedicularis in its center of diversity in the Hengduan Mountains of China (the eastern side of the Tibetan plateau), where nearly 300 species are endemic. Pedicularis in this region frequently overlap in their geographic ranges, flower synchronously during the short alpine summer, and share bumblebee pollinators. This combination of factors raises the potential for pollen transfer between different species, which can have negative fitness consequences (termed reproductive interference), and consequently impose strong selection on floral phenotypes. I combine genomic RADseq approaches above and below the species-level with field-based experiments and ecological studies and CBD Oil reviews to better understand the evolutionary consequences of these interactions.

Oaks – Coyne and Orr described oaks as “a worst case scenario of the biological species” due to their often blurred species boundaries resulting from hybridization. Whether as a consequence of hybridization, insufficiently variable markers, or sorting of ancestral polymorphisms in large populations of long lived trees, previous phylogenetic studies have shown great difficulty in resolving oak relationships at both shallow and deep evolutionary timescales. Applying genomic RADseq data we have resolved a backbone phylogeny of the American clade oaks (Hipp et al. 2014) and shown evidence of frequent hybridization among the live oaks which affects phylogenetic inference (Eaton et al. 2015), and which has likely persisted over millions of years (Cavender-Bares et al. 2015).

Viburnum – A model system for phylogenetic comparative methods in plants, and in particular historical biogeography and leaf trait evolution. We are using RADseq methods to infer deep-scale phylogenies, infer introgression between lineages, resolve polyploid lineages, and study replicate radiations of leaf forms among Viburnum in central and south America.



Software to assemble de novo RADseq loci from restriction-site associated sequence data (RAD,ddRAD,GBS,PEddRAD,PEGBS). Alignment clustering allows for indel variation to better align highly divergent samples, merge and trim methods canbe employed to rescue overlapping paired end data, and reverse complement clustering is available to improve GBS assemblies of short overlapping contigs.


Software to simulate fastQ formatted RAD, ddRAD or GBS data on an input species tree under a coalescent model. See example usage at this post.

Scientific data On Kratom and CBD

” Kratom (Mitragyna speciosa) is a tropical tree with a long history of traditional use in parts of Africa and Southeast Asia. Kratom is also known as Thom, Thang, and Biak. Its leaves and the teas brewed from them have long been used by people in that region to manage pain and opioid withdrawal and to stave off fatigue. Kratom is actually consumed throughout the world for its stimulant effects and as an opioid substitute (in form of tea, chewed, smoked, or ingested in capsules).” from nih.gov.

“Hemp oil is taken from food-grade hemp strains. These strains possess less than 0.3% THC, which is what gives you the “high” feeling when you smoke marijuana.

Hemp seeds come from the Cannabis sativa plant and contain an abundance of fatty acids, bioactive compounds, and other helpful nutrients. If you happen to buy full spectrum CBD oil for vaping, you can reap the benefits of additional plant compounds.” by organic newsroom

The program simrrls can be used to simulate raw (fastq format) sequence data on an input topology under the coalescent in a manner that emulates restriction-site associated DNA, with slight variations for different data types (e.g., RADseq, ddRAD, GBS, paired-end data).

RADseq was originally developed to generate data for bug testing pyrad and to create example RADseq data sets for use in tutorials. However, I can imagine other uses for it, such as investigating the effects of missing data, insufficient sequencing coverage and error rates on assembly results.

To use the program you will need to first install the Egglib Python module, used here to perform coalescent simulations.

Calling the script – simrrls

$ simrrls -h

optional arguments:
  -h, --help      show this help message and exit
  --version       show program's version number and exit
  -o outname      [str] output file name prefix (default 'out')
  -mc dropout     [0/1] allelic dropout from mutation to cut sites (default 0)
  -ms dropout     [0/1] allelic dropout from new cut sites in seq (default 0)
  -e error        [float] sequencing error rate (default 0.0005)
  -f datatype     [str] datatype (default rad) (options: rad, gbs, ddrad,
                  pairddrad, pairgbs)
  -I indels       [float] rate of indel mutations (default 0) ex: 0.001
  -l length       [int] length of simulated sequences (default 100)
  -L nLoci        [int] number of loci to simulate (default 100)
  -n Ninds        [int] N individuals from each taxon (default 1)
  -N Ne           [int] pop size (Ne for all lineages; default 5e5)
  -t tree         [str] file name or newick string of ultrametric tree
                  (default 12 taxon balanced tree w/ bls=1)
  -u mu           [float] per site mutation rate (default 1e-9)
  -df depthfunc   [str] model for sampling copies (default norm, other=exp)
  -dm depthmean   [int] mean sampled copies in norm, 1/m for exp (default 10)
  -ds depthstd    [int] stdev sampled copies, used with norm model (default 0)
  -c1 cut_1       [str] restriction site 1 (default CTGCAG)
  -c2 cut_2       [str] restriction site 1 (default CCGG)
  -i1 min_insert  [int] total frag len = (2*l)+insert (default 100)
  -i2 max_insert  [int] total frag len = (2*l)+insert (default 400)
  -r1 seed_1      [int] random seed 1 (default 1234567)
  -r2 seed_2      [int] random seed 2 (default 7654321)

Datatypes– RADseq is the default type for which a barcode and restriction site overhang are attached to the left side of single end reads. Depending on the data type selected simrrls will put cut sites and barcodes in the proper ends of sequences so that they emulate RAD, GBS, or ddRAD data, single or paired-end. The choice also effects how locus dropout occurs (i.e., one or two cutters present).

Allelic Dropout– There are two ways in which allelic dropout (mutation-disruption) can occur, each of which can be toggled. The first is mutations to the cut site recognition sequence (-mc). If this is turned on then an allele will be dropped if a mutation occurs within the length of the restriction recognition sites determined by the cutters (-c1 and -c2) and the data type (-f) which determines whether one or two cutters are used (e.g., rad is a single cutter, ddrad is double-cutter). The other form of mutation disruption occurs when mutations give rise to new cut sites within the length of a selected fragment (-ms). Here the total fragment length is determined by (-l) and the max insert length (-i2), and the probability of disruption by the cutters (-c1 and -c2), and the substitution rate (-N and -u).

Sequencing coverage and error– Another source of missing data in RADseq data sets is low sequencing coverage. You can set the sampling rate as the number of reads that are sampled from each haplotype. The mean (-dm) and standard deviation (-ds). To examine the effect sequencing rate has on base calls, etc., you could combine low coverage sequencing with a high error rate (-e).

Topology– Data are simulated under a Jukes-Cantor model with equal base frequencies. If there is no user-supplied topology (-t) then simrrls uses a default 12 tip topology, shown below. Branch lengths are in coalescent units. The outgroup taxon in the tree “X” is not included in the output, but is used to polarize mutations relative to an outgroup for creating indels.


Output – Two data files are created using the output name prefix (-o), which if it were ‘testrad’ would create testrad_R1_.fastq.gz and testrad_barcodes.txt. The first is a compressed fastq file with sequence data and the latter is a text file mapping barcodes to sample names. If you selected paired-end data it would create two sequence files, one with “_R1_” in the name and the other with “_R2_”. With these fastq data and a barcode map the data can then be assembled in pyrad.

Examples –

Modified population parameters:

$ simrrls -o test2 -N 1e6 -u 2e-8

Modified sequencing parameters:

$ simrrls -o test3 -L 5000 -l 200 -e 0.001 -dm 10 -ds 2

Modified library type (In this case allowing paired-end reads overlap):

$ simrrls -o test4 -f pairddrad -i1 -50 -i2 200

Modified topology:

$ echo "((a:1,b:1):1,c:2);" > treefile
$ simrrls -o test5 -t treefile

More info – Check out the git repository: (simrlls.py)



The benefit of pyRAD over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (vsearch) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.


pyRAD is intended for use with any type of restriction-site associated DNA. It currently supports RAD, ddRAD, PE-ddRAD, GBS, PE-GBS, EzRAD, PE-EzRAD, 2B-RAD, nextRAD, and can be extended to other types. Below is the download link as well as a number of tutorials. There is a “general use” pyRADtutorial which explains how to install and setup input files, and also tutorials with example data sets for different data types and analyses. pyRAD was initially described in the following publication (preprintjournal)