Program: GASP Description: Gapped Ancestral Sequence Prediction Version: 2.0.0 Last Edit: 08/03/18 Citation: Edwards & Shields (2004), BMC Bioinformatics 5(1):123.

Copyright © 2004 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: rje rje_obj rje_ancseq rje_seq rje_tree

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See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is purely for running the GASP algorithm as a standalone program. All the main functionality is encoded in the modules listed below. The GASP algorithm itself is now encoded in the rje_ancseq module. GASP may also be run interactively from the rje_tree module.

Input/Output

seqin=FILE : Fasta/ClustalW/Phylip Format sequence file [infile.fas].
nsfin=FILE : Newick Standard Format treefile [infile.nsf].
indeltree=T/F : Whether to output a text tree describing indel patterns [True]

GASP Model Options

fixpam=INT : PAM distance fixed to X [0].
rarecut=NUM : Rare aa cut-off [0.05].
fixup=T/F : Fix AAs on way up (keep probabilities) [True].
fixdown=T/F : Fix AAs on initial pass down tree [False].
ordered=T/F : Order ancestral sequence output by node number [False].
pamtree=T/F : Calculate and output ancestral tree with PAM distances [True].
desconly=T/F : Limits ancestral AAs to those found in descendants [True].
xpass=INT : How many extra passes to make down & up tree after initial GASP [1].

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Improved version with second pass.
    # 1.1 - Improved OO. Restriction to descendant AAs. (Good for BAD etc.)
    # 1.2 - No Out Object in Objects
    # 1.3 - Added more interactive load options
    # 1.4 - Minor tweaks to imports.
    # 2.0.0 - Upgraded to rje_obj framework for REST server.

GASP REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

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Available REST Outputs

seqin = Input sequence alignment [fas]
nsfin = Input phylogenetic tree (Newick) [nsf]
indeltree = [Optional] Text tree describing indel patterns. [txt]
anc.fas = Ancestral sequence prediction alignment [fas]
anc.txt = Text tree with ancestral nodes named and numbered [txt]
anc.nsf = Newick version of tree with ancestral nodes named and numbered [nsf]