This program is distributed in the hope that it will be useful, but withoutĪny warranty without even the implied warranty of merchantability or fitnessįor a particular purpose. License, or (at your option) any later version. License as published by the Free Software Foundation, either version 3 of the Redistribute it and/or modify it under the terms of the GNU General Public NJ tree python grapetree.py -p examples/simulated_data.profile -m NJĭistance matrix python grapetree.py -p examples/simulated_data.profile -m distanceĬopyright Warwick University This program is free software: you can Command line examples MSTree V2 python grapetree.py -p examples/simulated_data.profile -m MSTreeV2 The matrix is presented in PHYLIP format. Use the option '-method distance' to generate a distance matrix without calculating the tree. If a column labeled with "ID" presents, it will be used to correlate metadata with profiles, otherwise the first column will be used. The first row is required and describes the labels of the columns. This is only used for tree presentation in the standardalone version. The metadata file is either a tab-delimited or a comma-delimited text file. Note that GrapeTree supports only p-distance for the moment. Many sequence alignment tools, e.g., MAFFT and MUSCLE, use FASTA as a default format for their outputs. Aligned FASTAĪn aligned FASTA file contains multiple sequences of the same length in FASTA format. Use '-' or '0' to represent missing alleles. The first column needs to be unique identifiers for strains.Įach of the remaining rows presents a different strain. Collumn labels that start with a '#' are treated as comments and will not be used in downstream analysis. ![]() The first row is required and represents column labels. The profile file is a tab-delimited text file.įollow an example here: #Strain Gene_1 Gene_2 Gene_3 Gene_4 Gene_5 Gene_6 Gene_7. Detailed descriptions for -matrix, -recraft and -heuristic.check, -c Only calculate the expected time/memory requirements. ![]() n_proc NUMBER_OF_PROCESSES, -n NUMBER_OF_PROCESSES Tiebreak heuristic used only in MSTree and MSTreeV2 recraft, -r Triggers local branch recrafting.Ġ: ignore missing data in pairwise comparison.ģ: Absolute number of allelic differences. "distance": p-distance matrix in PHYLIP format. "RapidNJ": RapidNJ for very large datasets OR a fasta file containing aligned sequences. An input filename of a file containing MLST or SNP character data, h, -help show this help message and exit In brief, GrapeTree generates a NEWICK tree to the default output (screen) Usage - Command line module for generating Trees >grapetree -h To run tests, run pytests in the top level directory. Runtime behaviour can be configured in grapetree/config.py.ĭevelopers may wish to look at the JavaScript documentation (JSDoc). View a tree (newick or Nexus) or create a tree from an allele profile, just dragĪnd drop the file into the browser window. If at anytime you want to restart the page you can The program will automatically open your web browser and you will see the
0 Comments
Leave a Reply. |