SPIMAP (Spieces informed max a poseriori) http://compbio.mit.edu/spimap/ Matthew Rasmussen modified for WGD by Charles-Elie Rabier SPIMAPWGD is a version of SPIMAP which incorporates Whole Genome Duplications (WGD) events. ============================================================================= ABOUT SPIMAP is a phylogenetic program that uses a species tree to aide in reconstructing gene trees. It uses code from the SPIDIR phylogenetic library. SPIMAP citation: Rasmussen, Kellis. A Bayesian Approach for Fast and Accurate Gene-tree Reconstruction. Mol Biol Evol. 2011 Jan;28(1):273-90. Epub 2010 Jul 25. SPIDIR citation: Rasmussen, Kellis. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Research. 2007 This package includes the C++ source of the SPIMAP program and SPIDIR library as well as several library interfaces for C and python. ============================================================================= DEPENDENCIES SPIMAP has the following requirements: - GNU Scientific library (GSL) http://www.gnu.org/software/gsl/ - Python (2.5 or greater) http://python.org/ ============================================================================= INSTALL NOTE: Makefile installation will work best on UNIX or CYGWIN. To compile the SPIMAP stand-alone program use the Makefile. make To compile the SPIDIR C-library use: make lib Once compiled, to install the SPIMAP program (installs by default in /usr) use: make install To specify your own installation path use: make install prefix=/usr/local To use the training scripts (bin/spimap-prep-duploss, etc), python must be installed. ============================================================================= USAGE Running SPIMAPWGD with no arguments will print out its command-line usage: Usage: spimap [OPTION] -a,--align <alignment fasta> sequence alignment in fasta format -S,--smap <species map> gene to species map -s,--stree <species tree> species tree file in newick format -p,--param <params file> substitution rate parameters file -o,--output <output filename prefix> prefix for all output filenames -r,--recon Output reconciliation Sequence evolution model -k,--kappa <transition/transversion ratio> used for HKY model (default=estimate) -f,--bgfreq <A freq>,<C ferq>,<G freq>,<T freq> background frequencies (default: estimate) Dup/loss evolution model -D,--duprate <duplication rate> rate of a gene duplication (default=0.1) -L,--lossrate <loss rate> probability of loss (default=0.1) -LR,--lineagesatroot <param for lineages at the root> parameter for the geometric law, concerning the number of lineages at the root (default=0.95) -OB,--observingsomething <obssmthg> 1 for conditionning on observing something (default: 1) or 2 for at least one on the left and at least one on the right -P,--pretime <pre-speciation time parameter> lambda param of pre-speciation distribution (default=1.0) Search -i,--niter <# iterations> number of iterations --quickiter <quick iterations> number of subproposals (default=50) -b,--boot <# bootstraps> number of bootstraps to perform (default: 1) -g,--proposal-gene-topology <proposal type for gene tree topology> 1 for spr-neighbor, 0 for nni, 2 for SubtreeSlide (default: 2) --mcmc <mcmc> 1 for MCMC or 0 for MAP (default: 0) Information -V,--verbose <verbosity level> verbosity level 0=quiet, 1=low, 2=medium, 3=high --log <log filename> log filename. Use '-' to display on stdout. --treeSampled Output treeSampled --informationduploss Output losses, losses at WGD, duplications, duplications at WGD -v,--version display version information -h,--help display help information --help-debug display help information about debug options #============================================================================= # Examples see the examples on the website in order to learn how to run SPIMAPWGD