"proml" - 1 õppematerjal

Bioinformaatika arvestus ül

kitsch -Fitch-Margoliash tree drawing method with molecular clock neighbor -Neighbor-Joining and UPGMA tree drawing method Character based methods These programs read in the sequence alignment, and produce either one or multiple trees in the output files "outfile" and "outtree". dnapars -DNA parsimony dnapenny -DNA parsimony using branch-and-bound dnaml -DNA maximum likelihood without molecular clock dnamlk -DNA maximum likelihood with molecular clock protpars -Protein parsimony proml -Protein maximum likelihood Tree drawing These programs draw a tree from the specifications ("outtree") in the Newick-format. For example, the specification can be a file produced by the program dnaml. Drawgram and drawtree produce plotfile, whereas retree saves the result in a file "outtree" (so "outtree" can not be used as an input to this program). drawgram -Draws a rooted tree drawtree -Draws an unrooted tree retree -Interactive tree-rearrangement Consensus trees