Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/prottest.xml @ 0:5b9a38ec4a39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
1 <tool id="prottest" name="ProtTest 2.4" version="1.0">
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
2 <description>Selection of best-fit models of protein evolution.</description>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
3 <requirements>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
4 <requirement type="package">prottest</requirement>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
5 </requirements>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
6 <command interpreter="perl">
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
7 prottest_wrapper.pl -i $input -o $output
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
8 </command>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
9 <inputs>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
10 <param name="input" format="phylip" type="data" label="Input alignment (phylip recommended)"/>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
11 </inputs>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
12 <outputs>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
13 <data format="txt" name="output"/>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
14 </outputs>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
15 <tests>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
16 </tests>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
17 <help>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
18 **What it does**
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
19
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
20 ProtTest is a bioinformatic tool for the selection of the most appropriate model of protein evolution (among the set of candidate models) for the data at hand. ProtTest makes this selection by finding the model with the smallest Akaike Information Criterion (AIC) or Bayesian Information Criterion (BIC) score. At the same time, ProtTest obtains model-averaged estimates of different parameters (Posada and Buckley 2004) and calculates the importance of each of these parameters. ProtTest differs from its nucleotide homolog Modeltest (Posada and Crandall 1998) in that it does not include likelihood ratio tests (many models implemented in ProtTest are not nested).
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
21
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
22 ------
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
23
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
24 **Inputs**
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
25
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
26 Phylip recommended
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
27
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
28 ------
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
29
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
30 **Outputs**
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
31
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
32 Text file
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
33
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
34 -------
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
35
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
36 **Additional Information**
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
37
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
38 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
39 bitbucket.org
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
40
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
41 -------
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
42
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
43 **Citations**
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
44
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
45 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
46 consider citing the following.
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
47
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
48 Current Osiris Citation is here
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
49
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
50 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
51
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
52 Additional Citations for this tool
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
53
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
54 ProtTest 2.4 link: http://darwin.uvigo.es/software/prottest.html
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
55
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
56 Citation:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
57 Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics: 21(9):2104-2105.
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
58 </help>
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
59 </tool>