Software

Splits

The “splits” is an R package for species delimitation. It includes the generalized mixed Yule coalescent (GMYC) method developed by Tim Barraclough and myself. It delimits species using a single locus gene tree. Please visit the project website in R-forge to download and install the package.

http://r-forge.r-project.org/projects/splits

A web interface is also available at the HITS server maintained by Jiajie Zhang.

http://species.h-its.org/gmyc/

How to use “gmyc”

1. Installing “splits”
2. Running “gmyc” to delimit species
   • A slightly better plotting for delimitation results
3. Comparing GMYC-delimited species with other delimitation
   • If you want to check which species pairs match exactly when comparing 2 groupings…
4. Calculating support values of delimited species (in preparation)

Tr2

The “tr2” is a software for multilocus species delimitation. It is a fast method to delimit species with hundreds of gene trees. Its Python codes are available from my Bitbucket repository.

https://bitbucket.org/tfujisawa/tr2-delimitation

The original version of tr2 was written in Python2. Now, a Python3 version is available as well.

https://bitbucket.org/tfujisawa/tr2-delimitation-python3

A small example of delimitation with simulations is available here.

How to use “tr2”

1. Setting up a required environment for “tr2”
2. Installing “tr2”
3. Multilocus delimitation with “tr2” (Model comparison) 
4. Multilocus delimitation with “tr2” (Guide tree method) 

Also some notes about tr2 delimitation…

• Effects of reduced gene flow between populations
• Effects of reduced gene flow between populations II

 

Miscellaneous scripts

My blog posts include small scripts which are not important or original enough to be published separately. Please follow links if you are interested. If you find errors in the codes, please just let me know.

Large data handling

• Sampling a small number of elements from a huge file.(Python)
• Bootstrapping a very large file. (Python)

Sequence/tree processsing

• Converting a fasta alignment into SNPs.(Python)
• Extracting node annotations from a NEXUS tree file. (Python)
• Generating all possible topologies of rooted tree. (Python)

Sequence visualization

• Visual representation of an alignment matrix. (R)
• Visual representation of an alignment with ambiguous sites. (R)

Statistical analysis

• An example of MCMC sampling with PyMC (Python)

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