Phylogenetics

1. mafft

version 7.271

MAFFT is a multiple sequence alignment program for unix-like operating systems.
mafft in > out

1. raxmlHPC

version 8.2.4

Standard tool for Maximum-likelihood based phylogenetic inference.

1. iqtree

version 1.3.11.1 built Feb 1 2016 (quite old)

Efficient phylogenomic software by maximum likelihood

1. fasttreeMP

version version 2.1.8

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences

1. prottest

version 2.1

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand.

1. readal

version 1.2rev59

readAl reads protein or nucleotide alignments in several Multiple Sequence Alignment formats, including Phylip, Fasta, Clustal, NBRF/Pir, Mega and Nexus. The program detects automatically the input format and converts the alignment to other available formats.

1. trimal

version 1.2rev59

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment

trimal

1. PartitionFinder

PartitionFinder is software to select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.

1. MrBayes

version 3.2.6

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

please contact Łukasz B. before you will start using MrBayes

1. bmge

version 1.12

Selects regions in a multiple sequence alignment that are suited for phylogenetic inference. BMGE is able to perform biologically relevant trimming on a multiple alignment of DNA, codon or amino acid sequences.

bmge -?

1. concaterpillar.py

Assessment of congruence for protein alignment concatenation.