RNA-seq aligner

Genome modeling and design across all domains of life

Biological foundation modeling from molecular to genome scale

Cluster amino acid distributions for empirical distribution mixture models

A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

This is a new repository for Wammel, the phylogenetic hypothesis comparison tool.

Scoutknife is a naïve, whole genome informed phylogenetic robusticity metric

BaCoCa (Base Composition Calculator) is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used f…

BOSTIn is a new, user-friendly phylogenetic artifact identification package.

RCFV reader is a new software to quickly calculate normalised relative compositional frequency variability.

An R package to identify and classify duplicated genes from whole-genome protein sequence data

Improved Inference of Ortholog Groups using Hidden Markov Models

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

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

PhyIN sequence alignment trimming

Codon-Aware Multiple Sequence Alignments

mixed sample analysis

distance based phylogenetic placement

Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignments

Calculate summary statistics and manipulate multiple sequence alignments

🎄 spruceup

Explore spaces of phylogenetic trees

Analysis of Phylogenetics and Evolution

🌱 Base Classes and Functions for Phylogenetic Tree Input and Output

Leaderboard Comparing LLM Performance at Producing Hallucinations when Summarizing Short Documents

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

A program for divvying or partially filtering multiple sequence alignments