Reads in, edits and outputs phylogenetic trees. Executes duplication and subfamily determination. More details available
in documentation for HAQESAC, GASP and BADASP at http://www.bioinformatics.rcsi.ie/~redwards/
nsfin=FILE : load NSF tree from FILE
phbin=FILE : load ClustalW Format *.phb NSF tree from FILE
seqin=FILE : load sequence list from FILE (not compatible with useanc)
disin=FILE : load distance matrix from FILE (Phylip format for use with distance matrix methods) [
useanc=FILE : load sequences from ancestral sequence FILE (not compatible with seqin)
deflen=X : Default length for branches when no lengths given [0.1] (or 0.1 x longest branch)
*Note that in the case of conflicts (e.g.
useanc=FILE2), the latter will be used.*
autoload=T/F : Whether to automatically load sequences upon initiating object [
root=X : Rooting of tree (rje_tree.py):
- mid = midpoint root tree.
- ran = random branch.
- ranwt = random branch, weighted by branch lengths.
- man = always ask for rooting options (unless i<0).
- none = unrooted tree
- FILE = with seqs in FILE as outgroup. (Any option other than above)
rootbuffer=X : Min. distance from node for root placement (percentage of branch length)[
bootcut=X : cut-off percentage of tree bootstraps for grouping.
mfs=X : minimum family size [
fam=X : minimum number of families (If 0, no subfam grouping) [
orphan=T/F : Whether orphans sequences (not in subfam) allowed. [
allowvar=T/F: Allow variants of same species within a group. [
qryvar=T/F : Keep variants of query species within a group (over-rides
keepvar=LIST: Automatically keep variants for listed species (over-rides
groupspec=X : Species for duplication grouping [
specdup=X : Minimum number of different species in clade to be identified as a duplication [
9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [
group=X : Grouping of tree
- man = manual grouping (unless i<0).
- dup = duplication (all species unless groupspec specified).
- qry = duplication with species of Query sequence (or Sequence 1) of treeseq
- one = all sequences in one group
- None = no group (case sensitive)
- FILE = load groups from file
Tree Making Commands
cwtree=FILE : Make a ClustalW NJ Tree from FILE (will save *.ph or *.phb) [
kimura=T/F : Whether to use Kimura correction for multiple hits [
bootstraps=X : Number of bootstraps [
clustalw=CMD : Path to CLUSTALW (and including) program [''] * Use forward slashes (/)
fasttree=PATH : Path to FastTree (and including) program [
iqtree=FULLPATH : Path IQTree program including program [
phylip=PATH : Path to PHYLIP programs [''] * Use forward slashes (/)
phyoptions=FILE : File containing extra Phylip tree-making options ('batch running') to use [
protdist=FILE : File containing extra Phylip PROTDIST options ('batch running') to use [
maketree=X : Program for making tree [
- None = Do not make tree from sequences
- clustalw = ClustalW NJ method
- neighbor = PHYLIP NJ method
- upgma = PHYLIP UPGMA (neighbor) method
- fitch = PHYLIP Fitch method
- kitsch = PHYLIP Kitsch (clock) method
- protpars = PHYLIP MP method
- proml = PHYLIP ML method
- fasttree = Use FastTree
- iqtree = Use IQTree
- PATH = Alternatively, a path to a different tree program/script can be given. This should accept ClustalW parameters.
Tree Display/Saving Commands
savetree=FILE : Save a generated tree as FILE [
savetype=X : Format for generated tree file (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) [
treeformats=LIST: List of output formats for generated trees [
outnames=X : 'short'/'long' names in output file [
truncnames=X : Truncate names to X characters (0 for no truncation) [
branchlen=T/F : Whether to use branch lengths in output tree [
deflen=X : Default branch length (when none given, also for tree scaling) [
textscale=X : Default scale for text trees (no. of characters per deflen distance) [
seqnum=T/F : Output sequence numbers (if making tree from sequences) [
- Phylogenetic Tree class.
- Individual nodes (internal and leaves) for Tree object.
- Individual branches for Tree object.
History Module Version History
# 0.0 - Initial Compilation.
# 0.1 - Changed CladeList to lists inside tuple
# 0.2 - Completely reworked with a much greater OO focus
# 0.3 - No Out Object in Objects
# 1.0 - Better
# 1.1 - Added tree-drawing with ClustalW
# 1.2 - Bug fixing.
# 1.3 - Added separate maketree=PATH command to enable replacement of ClustalW tree drawing
# 1.4 - Added toggling of full sequence description in TextTree/EditTree
# 1.5 - Added ability to read in integer branch lengths
# 1.6 - Added PHYLIP tree making
# 1.7 - Modified text/log output. Added commandline scale option for text trees.
# 1.8 - Updating reporting of redundant duplication finding.
# 1.9 - Modified mapSeq() method to be more robust to different formats
# 1.10- Fixed some bugs and had a minor tidy.
# 2.0 - Updated code to be more inline with newer RJE modules. Fixed some bugs.
# 2.1 - Added tree savetype
# 2.2 - Added treeformats=LIST option to eventually replace savetype. Added te (TreeExplorer) format.
# 2.3 - Added specdup=X : Minimum number of different species in clade to be identified as a duplication 
# 2.4 - Added fasttree generation of trees.
# 2.5 - Added qryvar=T/F : Allow variants of query species within a group (over-rides allowvar=F). [False]
# 2.6 - Added PNG R variants.
# 2.7 - Added Improved NSF Tree reading.
# 2.8 - Added SVG and HTML Tree output.
# 2.9 - Added NWK output (=NSF output with different extension for MEGA!)
# 2.10- Added cleanup of *.r.csv file following R-based PNG generation.
# 2.11.0 - Modified for standalone running as part of SeqSuite.
# 2.11.1 - Tweaked QryVar interactivity.
# 2.11.2 - Updated tree paths.
# 2.12.0 - Added treeLen() method.
# 2.13.0 - Updated PNG saving with R to use newer code.
# 2.14.0 - Added cladeSpec().
# 2.14.1 - Fixed clustalw2 makeTree issue.
# 2.15.0 - Added IQTree.
# 2.16.0 - 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]
# 2.16.1 - Modified NSF reading to cope with extra information beyond the ";".
# 2.17.0 - keepvar=LIST: Automatically keep variants for listed species (over-rides allowvar=F). 
# 2.17.1 - Added forking to multithread IQ-TREE runs. Tweaked BUDAPEST R call.
rje_tree REST Output formats
for program documentation and options. A plain text version is accessed with
can be used to retrieve individual parts of the output, matching the tabs in the default
) output. Individual
elements can also be parsed from the full (
) server output,
which is formatted as follows:
... contents for OUTFMT section ...
Available REST Outputs
There is currently no specific help available on REST output for this program.