Currently this program only supports Linux.
cd into the root directory (containing the 'Makefile') and type:
./protspam [options] -l <filelist>
The program takes a plain text file containing the relative paths to each input dataset. To create your 'filelist' simply type:
ls -1 path/to/input/* > filelist
This will list each file in specified directory, one file per line.
-h/-?: print this help and exit -w <integer>: pattern weight (default 6) -d <integer>: number of don't-care positions (default 40) -s <integer>: the minimum score of a spaced-word match to be considered homologous (default: 0) -m <integer>: number of patterns used (default 5) -t <integer>: number of threads (default: omp_get_max_threads() ) -o <filename>: filename for distance matrix (default: DMat) -l <filename>: specify a list of files to read as input -z : if option is set, the pattern set used will be stored in patterns.txt" -p <filename>: filename of pattern set to load and reuse"
Sequence must be in FASTA format. All protein sequences of one proteome must be contained in one FASTA file.
>Protein1 RAKSDLKEASDKE.. >Protein2 ATSDLAGTASDKE.. >Protein3 ARNCQEFGSDSDW.. ..
Scientific publications using filtered spaced word matches should cite: Leimeister, C. A., Schellhorn, J., Schoebel, S., Gerth, M., Bleidorn, C., & Morgenstern, B. (2018). Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences. bioRxiv, 306142.
Word-based or "alignment-free" sequence comparison has become an active area of research in bioinformatics. Recently, fast word-based algorithms have been proposed that are able to accurately estimate phylogenetic distances between genomic DNA sequences without the need to calculate full sequence alignments. One of these approaches is Filtered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between species based on their complete or incomplete proteomes; our implementation is called Prot-SpaM. We show that Prot-SpaM can accurately estimate phylogenetic distances, and that our program can be used to calculate phylogenetic trees from whole proteomes in a matter of seconds. For various groups of taxa, we show that trees calculated with Prot-SpaM are of high quality. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM
You can download the datasets referenced in the paper here.