Bali-Phy is a software tool which uses Markov chains and Monte Carlo simulations for multiple alignments and building phylogeny. It also works out other parameters for unaligned sequences. The new version 3 of this software builds faster and larger trees. It has incorporated many new models like codon model.
The tool can analyze multiple genes simultaneously and has reduced the time for reconstruction of larger phylogenetic tree.The source code of the program has been written in C++. The source code can be downloaded from the following website: http://www.bali-phy.org.
Reference:
Redelings B.D.(2021)Bali-Phy version 3: model-based co-estimation of alignment and phylogeny. Bioinformatics 37(18):3032-3034.