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 csv2phyl.sh is obsolete.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