USAGE NOTES:

* Currently phybin ignores input trees with the wrong number of taxa.

* If given a directory as input phybin will assume all contained files are Newick trees.

Clustering Options

--bin

Use simple binning, the cheapest form of 'clustering'

--single

Use single-linkage clustering (nearest neighbor)

--complete

Use complete-linkage clustering (furthest neighbor)

--UPGMA

Use Unweighted Pair Group Method (average linkage) - DEFAULT mode

--editdist=DIST

Combine all clusters separated by DIST or less. Report a flat list of clusters. Irrespective of whether this is activated, a hierarchical clustering (dendogram.pdf) is produced.

Select Robinson-Foulds (symmetric difference) distance algorithm:

--hashrf

(default) use a variant of the HashRF algorithm for the distance matrix

--tolerant

use a slower, modified RF metric that tolerates missing taxa

Visualization

-g --graphbins

use graphviz to produce .dot and .pdf output files

-d --drawbins

like -g, but open GUI windows to show each bin's tree

-w --view

for convenience, "view mode" simply displays input Newick files without binning

--showtrees

Print (textual) tree topology inside the nodes of the dendrogram

--highlight=FILE

Highlight nodes in the tree-of-trees (dendrogram) consistent with the. given tree file. Multiple highlights are permitted and use different colors.

--interior

Show the consensus trees for interior nodes in the dendogram, rather than just points.

Tree pre-processing

--prune=TAXA

Prune trees to only TAXA before doing anything else. Space and comma separated lists of taxa are allowed. Use quotes.

-b LEN --minbranchlen=LEN

collapse branches less than LEN

--minbootstrap=INT

collapse branches with bootstrap values less than INT

Extracting taxa names

-p NUM --nameprefix=NUM

Leaf names in the input Newick trees can be gene names, not taxa. Then it is typical to extract taxa names from genes. This option extracts a prefix of NUM characters to serve as the taxa name.

-s STR --namesep=STR

An alternative to --nameprefix, STR provides a set of delimeter characters, for example '-' or '0123456789'. The taxa name is then a variable-length prefix of each gene name up to but not including any character in STR.

-m FILE --namemap=FILE

Even once prefixes are extracted it may be necessary to use a lookup table to compute taxa names, e.g. if multiple genes/plasmids map onto one taxa. This option specifies a text file with find/replace entries of the form "<string> <taxaname>", which are applied AFTER -s and -p.

Utility Modes

--rfdist

print a Robinson Foulds distance matrix for the input trees

--setdiff

for convenience, print the set difference between cluster*.txt files

--print

simply print out a concise form of each input tree

--printnorms

simply print out a concise and NORMALIZED form of each input tree

--consensus

print a strict consensus tree for the inputs, then exit

--matching

print a list of tree names that match any --highlight argument