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admixr

An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.

beast2-xml

Python code to generate BEAST2 XML files

chloroplast_genome_alignment

该项目包含一系列脚本，脚本可结合geneious软件对基因结构出现变化的叶绿体基因组编码区进行精确排序。The project includes a series of scripts that work with geneious software to alignment sequence the coding regions of the chloroplast genome where the gene structure has changed

dendropy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

discovista

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

get_homology

This simple script is used to remove suspected non-homologous sites that appear after alignment.

get_homology_from_proteinortho

Extract orthologous genes based on the output of Proteinortho v5.

hmmsearch_get_homology

使用hmmsearch程序，基于预先准备好的hmmer库，搜索几个物种之间的直系同源基因。

hyde

Hybridization detection using phylogenetic invariants

manim

Animation engine for explanatory math videos

phylip2eigenstrat

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

treepl

Phylogenetic penalized likelihood

wgd

Python package and CLI for whole genome duplication analyses