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animal_tree_root

anomaly_zone

Detecting the anomaly zone in trees - modified from Linkem et al 2016

aster

Accurate Species Tree EstimatoR series: a familiy of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

avp

Automatic evaluation of HGTs

bayescode

Mutation-Selection phylogenetic codon models to detect site-specific adaptive evolution or to infer long-term effective population size

branch_length_models

caastools

CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.

cactus

Official home of genome aligner based upon notion of Cactus graphs

cagee

Computational Analysis of Gene Expression Evolution

castles

Coalescent-Aware Species Tree Length Estimation in Substitution-units

cblaster

Find clustered hits from a BLAST search

chromomap

:exclamation: This is a read-only mirror of the CRAN R package repository. chromoMap — Interactive Genomic Visualization of Biological Data

clan_check

Check trees for compatibility with defined groupings in unrooted trees - "The incontestable clan test"

clinker

Gene cluster comparison figure generator

colabfold

Making Protein folding accessible to all!

compleasm

A genome completeness evaluation tool based on miniprot

complexheatmap

Make Complex Heatmaps

ddbd-tree-prior

Estimate parameters for birth-death speciation model from molcular phylogenies

dissectingfactors

Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models

emma

an ensemble usage of MAFFT-linsi --add on large datasets

erc

esl

Evolutionary Sparse Learning

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

evolclust

Evolcust retrieves groups of genes that appear clustered together in groups of species

evoscope

Inference of correlated evolution on phylogenetic trees

fastortho

fastral

A hybrid summary method for reconstructing species tree from gene trees

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

galba

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.

gene-neighborhoods