PhylIP

PHYLIP is a free software package for inferring phylogenies. The name PHYLIP is an acronym for "The Phylogenetic Inference Package". It was developed by Joseph Felsenstein and is one of the most widely used phylogenetic software packages. PHYLIP offers a comprehensive suite of programs for performing various phylogenetic analyses, including distance matrix methods, maximum likelihood, and parsimony.

The package is designed to be portable and runs on a wide variety of computer systems, including Unix, Linux, macOS, and Windows. It has been in continuous development since its initial release in 1980, with regular updates to incorporate new algorithms and improve existing ones. PHYLIP's command-line interface makes it suitable for scripting and integration into larger bioinformatics workflows.

Key features of PHYLIP include the ability to analyze DNA, RNA, protein, and restriction site data. It supports a range of tree-building methods, such as Neighbor-Joining, UPGMA, Felsenstein's bootstrap, and various parsimony algorithms. The output of PHYLIP programs can be visualized using other phylogenetic software. Due to its long history, extensive functionality, and free availability, PHYLIP remains a valuable tool for researchers in evolutionary biology, genomics, and related fields.