Install notes for get_phylomarkers

This file lists the software components of the get_phylomarkers pipeline and briefly describes how to install them.

Scripts distributed through GitHub

Bash scripts

run_get_phylomarkers_pipeline.sh (the main script to run the pipeline)
run_pexec_cmmds.sh
run_parallel_molecClock_test_with_paup.sh

Perl scripts

add_labels2tree.pl
add_nos2fasta_header.pl
concat_alns_local.pl
convert_aln_format_batch_bp.pl
pal2nal.pl
popGen_summStats.pl
rename

R scripts

compute_suppValStas_and_RF-dist.R
run_kdetrees.R consense

External dependencies: second party binaries to be installed by the user.

NOTE: the corresponding binaries, after installation, shoud be found in the list of directories hold in the $PATH variable.

clustal omega. Multiple sequence alignmet software. Sievers et al. 2011. On Ubuntu try: 'sudo apt-get install clustalo'
pexec. Execute processes in parallel on multicore machines. On Ubuntu try: 'sudo apt-get install pexec'
Phi test. Recombination test software. Bruen et al. 2006
FastTree. Fast maximum-likelihood tree searching program. Price et al. 2010. On Ubuntu try: 'sudo apt-get install fasttree'
paup*. Multipurpose phylogenetics software developed by David Swofford and colleagues.