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biopython
biopython

Official git repository for Biopython (originally converted from CVS)

8.5M 5K 2K
etetoolkit
ete3

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.

166K 876 226
tskit-dev
tskit

Population-scale Ancestral Recombination Graph (ARG) library

95K 183 83
cogent3
cogent3

Comparative Genomics Toolkit 3

25K 134 67
jlsteenwyk
phykit

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

13K 84 8
holmrenser
nj-py

Neighbor-Joining phylogenetic tree inference. Auto-detects DNA/protein, supports multiple substitution models and bootstrap.

11K 1 0
neherlab
phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

9K 251 60
jlsteenwyk
clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

7K 89 5
albertyw
itolapi

Python API for the Interactive Tree of Life (iTOL)

5K 37 11
HuttleyLab
diverse-seq

Tools for analysis of sequence divergence

5K 15 4
theosanderson
taxoniumtools

Generate files for taxonium

4K 131 28
Ecogenomics
gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

3K 593 97
evolbioinfo
pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

3K 39 7
faridrashidi
trisicell

No description available

3K 14 2
hallamlab
treesapp

TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.

2K 26 4
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
jjmccollum
teiphy

Converts TEI XML collations to NEXUS and other formats

2K 21 5
theosanderson
chronumental

Estimating time trees from very large phylogenies

2K 28 7
matsengrp
gctree

phylogenetic inference of genotype-collapsed trees

2K 18 2
AndreaRubbi
pear-ebi

Calculates distances of trees in large collections. Embeds distances and plot the embeddings with dynamic interfaces.

1K 6 3
michaelgruenstaeudl
plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across thousands of plastid genomes using associative arrays

1K 1 0
david-schaller
asymmetree

Simulator for species and gene trees with asymmetric evolution rates

1K 7 2
evogytis
baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

1K 119 33
DeadlineWasYesterday
bionick

Software for manipulating Newick strings and adding phylogenies to Matplotlib visuals.

916 0 0
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