category: Molecular Markers

programs:

• beagle - Phasing genotypes and imputing ungenotyped markers
• blmarker - bioLegato interface for discrete state data (eg. molecular markers)
• csv2phyl.sh - >>> csv2phyl.sh is obsolete. Instead, use phylcnv.py which handles a larger number of file formats
• dollop - Discrete data parsimony method of DOLLO
• drawgram - Draw cladograms
• drawtree - Draw radial trees
• fitch - Distance trees - Fitch/ Margoliash
• genographer - Score markers from gel images
• kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
• Mapmaker - Create genetic maps using marker and phenotype data
• MapmakerQTL - Create maps for QTL data
• mGDE - GDE interface for discrete state data (eg. molecular markers)
• mix - Mixed method discrete character parsimony
• neighbor - Distance trees - Neighbor-Joining/UPGMA
• phylcnv.py - Convert Phylip files to and from other formats
• restdist - Compute distance matrices for discrete data
• restml - Maximum likelihood phylogeny for discrete data
• treedist - Calculate distance between trees
• v_concat - Concatenates a set of sequence alignments.
• v_demograph - Estimates demographic parameters (effective population size, growth rate) by maximizing the coalescent prior for a single given clocklike tree.
• v_disttree - Tree methods dealing with distance matrices.
• v_evolve - Generates artificial data sets for a tree and a model of sequence evolution (available models are the same as in MLTREE and MLDIST)
• v_mldist - Computes pairwise maximum-likelihood distance matrices for nucleotide, amino acid, and two-state data under a variety of substitution models
• v_mltree - Computes likelihoods of trees under a variety of substitution models (see MLDIST)
• v_reroot - Reads a treefile (NH format) and reroots the tree, making node the new root.
• v_rewrite - Reads a data set and reformats it into various formats
• v_showtree - Reads treefile (NH format), generates ASCII picture, and computes distance matrix induced by branch length.
• v_splitcodon - Separate 1st, 2nd, 3rd codon positions of an alignment into separate file.
• v_treecomp - Reads two trees, each from a different file, and computes the Robinson Foulds score (topological distance measure based on splits).