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Phylogenomics Python Packages

Python packages with the GitHub topic phylogenomics. Sorted by relevance, with stars and monthly downloads.
jlsteenwyk
clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

11K 89 5
jlsteenwyk
phykit

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

9K 85 9
moshi4
aniclustermap

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

616 93 12
natapol
kitsune

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

539 15 3
TheBrownLab
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.

506 36 16
moshi4
cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

415 36 3
JLSteenwyk
orthofisher

orthofisher

408 41 1
merlyescalona
ngsphy

NGSphy: phylogenomic simulation of next-generation sequencing data

402 14 6
moshi4
fastdtlmapper

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

327 17 5
jlsteenwyk
orthosnap

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

309 30 1
HSecaira
tmarsel

Repository for TMarSel

237 1 0
pblischak
phyde

Hybridization detection using phylogenetic invariants

216 52 14
K-nie
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.

198 1 0
DeadlineWasYesterday
phyca

phylogeny and collinearity aware assembly evaluation toolkit.

122 1 0
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