category: Molecular Markers

programs:

• 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 csv2phyl.sh is obsolete.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
• 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