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

kitsune

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

aniclustermap

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

phylofisher

PhyloFisher is a software package for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms.

orthofisher

orthofisher

orthosnap

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

ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

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.

phyde

Hybridization Detection Using Phylogenetic Invariants

tmarsel

Repository for TMarSel

phyca

Universal ortholog based Phylogenomic toolkit.