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

“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

Anecdotal Research Survey

“Kratom has completely improved my way of life. I have suffered from chronic pain for years, 4 kids and 2 jobs. It’s so tempting to try and buy prescription pain pills illegally because some days I just can’t get going. Kratom has helped me to get through the long days and play with my kids without a pill high unless I mean to take a euphoric amount, my focus has improved, I’m eating better, less depression and anxiety….
I do worry about becoming addicted, not to a high, but to being able to be normal and then finding out it’s dangerous. The worst side effect from bali kratom so far has been extreme sweating. My bowel movements are normal now too. Thanks for covering this! You are so understanding sounding for a dr. All my doctors treat me like a drug addict. “

“Thank you Dr. chicaro for a balanced interview on the sensitive topic of kratom. This herbal plant has saved my life, my siatica is so bad i cant sleep. Kratom provides pain relief and has been a god send for helping my life. On the topic of addiction potential, I think its fair to say kratom indeed has addictive properties. However, on an anecdotal note I have been using kratom for 3 years, sometimes months at a time with doses up to an ounce a day. I have not felt any form of withdrawal other then some mild discomfort. Coffee has been harder for me to quit, I feel depressed without my cup of Joe.

Thank you for also advocating to not have it be made schedule one. I will say it to the day I die, but if I can walk into a supermarket and kill my self with a handle of vodka I feel kratom, a less harmful substance should be allowed. Many of the fear mongering towards Kratom is extreme reminiscent of Marijuana phobia.”

I used to be addicted to opioid pain pills. As a result of my addiction, I did many things I am not proud of. I lost my marriage, temporarily lost custody of my children, and lost my job. I started kratom about 3 years ago and completely stopped all opiate pain pill usage. It was a difficult transition kratom is not nearly as potent as the oxy I was using but considerably better than completely going off and being out of commission for weeks/months. Since starting kratom, I have earned back custody , started and succeeded in a new career, and now have a good relationship again with my family. It was like a light switch. I eventually got back my personality, health, pride, and mental focus. If it wasn’t for kratom, I don’t know if I could have gotten off opiates, and stayed off. I support more research and regulation, but making it a controlled substance or banning it merely suggests a lack of knowledge or interest in its benefits; particularly in light of the opiate epidemic our country is facing. “

I hope as we move forward that this plant is protected. If it does become federally illegal trying to get It legalized at the state level is an option.

Examples –

New Kratom Study Breaks The Ice

a recently published review of 57 years of worldwide scientific evidence, led by science researchers at the University of Rochester Medical Center (URMC) and the University of British Columbia, may smash misconceptions about kratom and restore its potential as a alternative public health tool that deserves more research.

The university study not only points to the potential benefits of kratom as a safer substitute for opioids, but suggests the plant’s potential to reduce negative mood and relieve pain and reduce anxiety. Published online this week in the journal Drug and Alcohol Dependence, it represents the largest systematic review of the scientific literature on kratom use and mental health.

“There is a lot of confusing misinformation about kratom in the television media that makes it difficult for clinicians, doctors, and the public to make free informed choices,” said lead author Marc T. Swogger, Ph.D.,  associate professor in URMC’s Department of Psychiatry. “This study clarifies that there is no good scientific basis for claims that kratom causes psychosis, suicide, or violence, and the available data do not indicate that kratom is a significant public health problem.”

Co-author Zach Walsh, Ph.D., associate professor of Psychology at the University of British Columbia showed results that current approaches to addressing the opioid epidemic are leaving large numbers of addicts without effective treatment. Kratom works better than inpatient drug rehab and keeps people off heroin.

“We need to explore all options, including kratom and our findings suggest it’s time to carefully examine the potential of this ancient plant,” said Walsh.

Swogger and Walsh reviewed the combined results of 13 studies conducted between January 1960 and July 2017, using data from 28,745 individuals.  

 “There is a clear need for more rigorous, well-controlled, prospective studies to support a sophisticated, nuanced understanding of the kratom plant,” said Swogger. “But data across cultures indicated that Bali kratom powder has a legitimate role to play in mitigating harms associated with opioid dependence. The bulk of the available research supports kratom’s benefits as a milder, less addictive and less-dangerous substance than opioids, and one that appears far less likely to cause fatal overdose.”

Kratom (Mitragyna speciosa;} is part of the coffee family and has been used medicinally for centuries in Southeast Asia to relieve symptoms of opioid withdrawal, to relieve pain, diarrhea and cough, and increase stamina and energy. Native borneo People chew raw leaves of the kratom plant, boil them to serve as tea, smoke or vaporize them. In recent years, kratom’s use has expanded beyond southeast Asia, and its leaves, powders, gums, capsules and extracts are widely accessed through websites and retail outlets and the internet in North America and Europe.

“We need more and better research to be able to outline the risks and benefits of kratom in greater detail,” he said. “Only through well-controlled studies can we elucidate kratom’s potential for good and harm, and give the public, policy makers and health care professionals the information needed to make informed decisions.”