In reconstruction of phylogenetic trees, automatic annotation from a given sequence database is quite important. One of our objects is inference of evolution by means of interpreting a phylogenetic tree rather than reconstruction of a phylogenetic tree itself. In this sense, annotation of the tree is an essential process in this study. However, when the number of sequences is large, it is virtually impossible to annotate without erroneous description by hand. The automatic annotation will make us free from such difficulty.
In DeepForest, annotating trees is carried out as follows:
Programs make_destbl and make_ph have been prepared
to annotate a tree. When we have a tree in the phylip format, for example
mhc.phb, this tree is annotated as follows:
make_records mhc.dat mhc.pl extract_fields mhc.pl mhc.ent.pl ENTRY TITLE make_destbl mhc.ent.pl mhc.des # In the current version, some operations are needed by hand here. # Replace all parentheses with square brackets, and replace all # commas with slashes in mhc.des. make_ph mhc.des mhc.phb mhc.des.phb
An annotated tree (mhc.des.phb) is shown in fig. 1.3.