Phylogenomics Python Packages

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

phykit

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

aniclustermap

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

kitsune

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

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.

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

orthofisher

orthofisher

ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

fastdtlmapper

Fast genome-wide DTL(Duplication-Transfer-Loss) event mapping tool

orthosnap

orthosnap, identify orthologous subgroups of genes in large orthologous groups of genes.

tmarsel

Repository for TMarSel

phyde

Hybridization detection using phylogenetic invariants

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.

phyca

phylogeny and collinearity aware assembly evaluation toolkit.