evolbioinfo

https://github.com/cov-lineages/pangolin

Simulation of rooted phylogenetic trees under a given Multitype Birth–Death (MTBD) model.

RAxML Next Generation: faster, easier-to-use and more flexible

Set of command line tools to manipulate phylogenetic trees

Goalign is a set of command line tools to manipulate multiple alignments

Plotting tool for long read sequencing data and alignments.

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

treestructure R package (Volz et al. bioRxiv 704528; doi: https://doi.org/10.1101/704528)

A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.

https://github.com/RasmussenLab/vamb

SPAdes is an assembly toolkit containing various assembly pipelines

IRMA: Iterative Refinement Meta-Assembler

HMMER: biosequence analysis using profile hidden Markov models

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

FastTree infers approx-max-likelihood phylogenetic trees from alignments of nt or aa sequences

https://github.com/cbg-ethz/shorah/

MUSCLE multiple alignment software