Phylogenomics Python Packages

phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

zombi2

A Python library for simulating the evolution of species, genomes, sequences and traits

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

phylofisher

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.

kitsune

a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.

orthofisher

a broadly applicable tool for automated gene identification and retrieval

orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes

ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

phyde

Hybridization detection using phylogenetic invariants

fastdtlmapper

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

genome-format-converters

A unified Python CLI for 30 bioinformatics file-format conversions (VCF, GFF3, GTF, BED, GenBank, FASTA, FASTQ, BAM, EIGENSTRAT, PLINK, MAF, MUMmer, HMMER, Newick) with consistent flags, batch mode, and a published Stage 1 benchmark vs convertf, plink2, AGAT, gffread, UCSC, EMBOSS, pyhmmer.

qrstar

Rooting species trees under the multi-species coalescent model

tmarsel

Repository for TMarSel

zombi2-core

A Python library for simulating the evolution of species, genomes, sequences and traits

phyca

phylogeny and collinearity aware assembly evaluation toolkit.