Running SVD quartets species tree estimation in PAUP* Linux command line.

The program PAUP* is a mainstay of phylogenetic analysis and is still under active development. A test version implements the SVD quartets method of species tree estimation using your concatenated alignment file - quartets are commonly used in phylogenetic species tree estimation (e.g. ASTRAL; Mirarab and Warnow, 2015) where the inputs are multiple gene tree bootstrap trees estimated by other means such as RAxML (Stamatikis, 2006).This is distinct in that each site is assumed to have its own genealogy drawn from the coalescent model and all sites in the alignment are used. I was running this over a lot of different alignments representing various loci and site filtering strategies.

To run in Linux:
Download the Linux version.
Extract to a folder with the alignments in nexus format. Use PAUP (command ToNexus ?) Geneious, R or AMAS (Borowiec 2016) or other programs to convert from phylip or fasta to nexus. Concatenation can be done using AMAS or SequenceMatrix or other programs (Vaidya et al., 2011).
Now start:
Open a terminal and cd to the directory with the program and nexus files make sure its executable chmod+x.
> paup4a149_ubuntu64
paup> ? #this gives you the available commands
paup>svdq ? #gives you the settings and commands for the SVD quartets
paup> Set warnReset=no #this means when you run multiple runs you don't get warning prompts about opening a new data file.
paup> Execute your_alignment_in_nexus_format.nex; SVDQuartets nthreads=4 evalQuartets=random bootstrap=yes TreeFile='output_file_name_for_boots.trees'; SaveTrees file=output_file_name_for_consensus.tre; ClearTrees;# don't use clear trees unless you are running multiple runs

If you have lots of runs to do you can paste this last command [ClearTrees] with appropriate changes to the alignment source files and output file names. The bootstrap defaults to 100 iterations, and if you change evalQuartets=All then all the possible quartets will be tried, it defaults to certain small percent - this is proportional to the number of taxa. With the default quartet evaluation proportion (my alignment of 138 thousand bases and 104 taxa took about 4 hours to run.

Literature
Borowiec, M.L. 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics J. J. Li [ed.],. PeerJ 4: e1660.
Chifman, J., and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30: 3317–3324.
Mirarab, S., and T. Warnow. 2015. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 31: i44–i52.
Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-1 based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690.
Swofford, David L. "{PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4.}." (2003).
Vaidya, G., D.J. Lohman, and R. Meier. 2011. SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information. Cladistics 27: 171–180.

Concatenate fasta files and add file name to each line

grep '.*' file*.* >file_out.txt

Often we need to concatenate many files where each file represents a separate analysis, or DNA alignment or whatever. This use of grep adds the file name to each line of output. I needed this to create a database of locus by locus alignments for searching in Geneious.