Rationale:
Confadd adds confidence information (typically bootstrap values)
to an existing phylogenetic tree. A typical use case would be if
you run bootstrap replicates of a phylogeny and then generate a
consensus tree from the replicates. The consensus tree could be
rerun by a program such as protpars of proml to obtain branch
lengths, but you would lose the replicate numbers.
Confadd reads a tree, and also reads a file of replicate trees,
recalculates the bootstrap values for how often clades in the
replicate trees match clades in the target tree, and outputs the
target tree with both branch lengths and boostrap values to a
phyloXML file. The phyloXML file can be viewed using
Archaeopteryx.
Input:
target tree file (selected in bltree) - The tree to
which you want to add bootstrap values
bootstrap tree file - File containing
all trees from a boostrapped phylogeny (eg. protpars, proml,
dnapars, dnaml) using "save raw trees to a separate file". Note:
The bootstrap tree file is NOT a single tree with bootstrap
numbers. It is simply a file of trees in any of the formats
supported (eg. nh, newick, phylloxml).
Parameters:
Strict (-s, default: yes) - all nodes between 'target' and
'evaluators' must match
Normalize to this number (-n, default:100) - If set to 100,
bootstrap values will be a percentage of trees in which a
particular clade appears. For example, if there were 500 replicate
trees, a clade which appeared in 250 of the replicates would have
a replicate value of 50. Most publications normalize to 100, but
you can alternatively set this to the actual number of trees
considered.
WHERE TO SEND OUTPUT - By default, bltree will run confadd and
send the output tree to Archaeopteryx. If you choose "phyloXML
file" output will be written to a file whose name is specified in
the "raw filename" field, with the extension .phyloxml.
Output:
outfile - A
phyloxml file. Phyloxml is a feature
rich format for representing information associated with
phylogenetic trees.