Hilmar at 14:08, 1 August 2011

2011-08-01T14:08:37Z

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= PhyloWays: a list of interpreted phyloinformatics workflows =

This is intended to house a reference set of pairs, where each pair consists of
# a publication reporting a phylogeny
# a more precise or formal description of the methods

This reference set is developed in the hope it will be useful for various projects:
* developing the vocabulary support to annotate phylogenetics workflows
* developing an annotation tool to create phylogenetic records that satisfy a MIAPA-like standard
* testing natural-language-processing (NLP) tools to extract methods information from published papers
* creating an archive where users share, ''like'', comment, and link to workflow descriptions

== overview ==

== guidelines ==

== cases ==

=== Angiosperm phylogeny (Soltis, et al, 2011) ===
'''Publication'''
Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS, et al. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot 2011:ajb.1000404. - http://www.amjbot.org/cgi/reprint/ajb.1000404v1

'''Data''': concatenated alignments for a superset of 14loci/17 genes (nucleotide sequences) sampled from 640 species. Genes included 18S rDNA (nuc), 26S rDNA (nuc), atpB (cp), atp1 (mito), matK (cp), matR (mito), nad5 (mito), ndhF (cp), psbBTNH (cp 4 gene region), rbcL (cp), rpoC2 (cp), rps16 (cp), rps3 (mito), and rps4 (cp).

'''Alignment method''': MAFFT used to align each of 14 loci; "adjustments were made by eye when there were obvious alignment errors due to particularly divergent or “ gappy ” sequences"; Sites (columns) with > 50% missing data (including gaps due to indels) were removed using Phyutility (Smith and Dunn, 2008). All or subsets of gene alignments concatenated for phylogenetic analysis.

'''Tree estimation''': Independent MP and ML analyses performed the following data matrices; nuclear rDNA genes; cp genes; mito genes; nuclear+cp genes; all 17 genes.
# '''Method (1)''' - ML; 10 independent runs for each data matrix.
#* Program - RAxML (vers. 7.1; Stamatakis, 2006 ).
#* Model of sequence evolution - GTRGAMMA with parameters estimated separately (unlinked) for each gene partition.
#* Method for evaluating support - 100-300 bootstrap replicates
# Method (2) - MP parsimony ratchet with 50 independent replicates, each run for 500 iterations each; MP tree estimates as majority rule of best trees from each replicate; tree only shown for 17 gene supermatrix.
#* Program - SeqBoot (Phylip; Felsenstein, 2005), PAUPRat ( Sikes and Lewis, 2001 ) and PAUP* 4.0b10 ( Swofford, 2002 ).
#* Method for evaluating support - bootstrap - 500 bootstrap datasets generated using SeqBoot. A PAUPRat-generated ratchet file generated for each pseudoreplicate and run for a single 500-iteration search.

'''Additional comments''': Trees available in TreeBASE - http://www.treebase.org/treebase-web/search/study/analyses.html?id=11267 ; Polyosma mtDNA loci omitted from analysis as contaminant after assessing discordance with other loci; Cardiopteris atp1 suspected as a contaminant, but retained.

'''semi-formalized description'''

The main descriptive statement
publication Pub1 reports PhylogenyResult1.1 and PhylogenyResult2.1

About the publication
Pub1 has_authors "Soltis DE", "Smith SA", "Cellinese N" . . .
Pub1 has_citation "Am J Bot 2011:ajb.1000404" . . .
Pub1 has_URL . . .

About phylogeny result 1.1, which is a consensus tree?
the value is either concrete (a newick tree) or a pointer (to a treebase accession or a nexml object)
PhylogenyResult1.1 has_value . . . < concrete or referenced_by pointer >
PhylogenyResult1.1 has_input PhylogenyResult1.0
PhylogenyResult1.1 has_method MajorityRuleConsensus # ?? not sure
PhylogenyResult1.1 has_method_details "100 to 300 bootstrap replicates"

PhylogenyResult1.0 has_value NA # we are not showing all the bootstrap trees
PhylogenyResult1.0 has_input Alignment1.1
PhylogenyResult1.0 has_method Method1

About phylogeny result 2.1, which is a consensus tree
PhylogenyResult2.1 has_value . . . < concrete or referenced_by pointer >
PhylogenyResult2.1 has_input PhylogenyResult2.0
PhylogenyResult2.1 has_method MajorityRuleConsensus
PhylogenyResult2.1 has_method_details "not sure about this"

PhylogenyResult2.0 has_value NA # we are not showing all the bootstrap trees
PhylogenyResult2.0 has_input Alignment1.1
PhylogenyResult2.0 has_method Method2

'''ALIGNMENTS'''
About Alignment1.1, which is an edit from Alignment 1.0, which is a concatenation
Alignment1.1 has_value . . . < concrete or referenced_by pointer >
Alignment1.1 has_input Alignment1.0
Alignment1.1 has_method Pruning
Alignment1.1 has_method_details "delete sites with >50% missing data"

Alignment1.0 has_value . . . < concrete or referenced_by pointer >
Alignment1.0 has_input Alignment2.1, Alignment3.1 . . . Alignment15.1
Alignment1.0 has_method Concatenate

About Alignment2.1, a component alignment edited from a MAFFT alignment
Alignment2.1 has_value . . . < concrete or referenced_by pointer >
Alignment2.1 has_input Alignment2.0
Alignment2.1 has_method EditByHand
Alignment2.1 has_method_details "remove divergent or gappy sequences"

Alignment2.0 has_value . . . < concrete or referenced_by pointer >
Alignment2.0 has_input . . . < list of GenBank accessions, ideally >
Alignment2.0 has_method MAFFT
Alignment0.0 has_method_details NA

Alignments 3.1 to 15.1 are similar-- each one is a possibly edited version of a MAFFT alignment for an individual set of sequences.

'''PHYLOGENY METHODS'''

Method1 has_attributes
* software RAxML
* software_version 7.1
* objective_function maximum_likelihood
* sitewise_model SiteWiseModel1
* among_site_model AmongSiteModel1

SiteWiseModel1 has_attributes
* GTR

AmongSiteModel has_attributes
* gamma
* partitions

Method2 has_attributes
* software PAUPRat
* software PAUP
* software_version 4.0b10
* objective_function maximum_parsimony
* search_method parsimony_ratchet

=== another case ===

[[Category:MIAPA]]

MIAPA/PhyloWays - Revision history

Hilmar at 14:08, 1 August 2011