GCtree specifications


Unique identifier OMICS_29148
Name GCtree
Alternative name Genotype-Collapsed tree
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A sequence for each observed individual/cell, and an additional sequence containing the ancestral genotype of all observed sequences.
Input format FASTA,PHYLIP
Output data A text file mapping collapsed sequenced ids to cell ids from the original input file, one with ids to their abundances, a phylip alignment file of collapsed sequences for computing parsimony trees, a directory of parsimony tree output from PHYLIP's dnapars, a rendered tree images for each of the parsimony trees, an histogram of genotype abundances, a rank plot of GCtree likelihoods for the parsimony trees, a log file containing parameter fits, numerical likelihood results, and any other program messages, and a python pickle file containing the parsimony trees.
Output format PDF+SVG
Operating system Unix/Linux, Mac OS
Programming languages Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
scons, scipy, matplotlib, seaborn, pandas, biopython, ete3, nestly, PHYLIP, X11 or xvfb-run, seqmagick
Maintained Yes




No version available



  • person_outline Frederick A. Matsen
  • person_outline Vladimir Minin

Publication for Genotype-Collapsed tree

GCtree institution(s)
Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA; Department of Statistics, University of California, Irvine, CA, USA
GCtree funding source(s)
Supported in part by a National Institutes of Health National Human Genome Research Institute Genome Training Grant (5T32HG000035-23), National Institutes of Health grant R01 AI119006, National Institutes of Health grant R01 GM113246 and National Science Foundation grants CISE-1564137 and CISE1561334, in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation, as well as by National Institutes of Health grant R01 AI120961 (PI Overbaugh).

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