Data from: Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa

Reich A, Dunn C, Akasaka K, Wessel G

Date Published: March 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.22sf3

 

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Title Dense supermatrix
Downloaded 11 times
Description This phylip format supermatrix alignment was generated using agalma 0.3.5 and orthologous genes were identified by pair wise BLASTp followed by clustering using MCL. The dense supermatrix has all 30 taxa and 70% matrix occupancy, with 1,125 peptide sequences and 101,652 amino acid sites.
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Download README.txt (1.314 Kb)
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Title Sparse supermatrix
Downloaded 4 times
Description This phylip format supermatrix alignment was generated using agalma 0.3.5 and orthologous genes were identified by pair wise BLASTp followed by clustering using MCL. The sparse supermatrix has all 30 taxa and 34% matrix occupancy, with 4,645 peptide sequences and 630,945 amino acid sites.
Download supermatrix.sparse.phylip (32.57 Mb)
Download README.txt (1.314 Kb)
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Title Species tree from PhyloBayes analysis on dense supermatrix
Downloaded 5 times
Description Baysian phylogenetic analyses were done with PhyloBayes 1.3b-mpi on the dense supermatrix using the CAT-GTR model with the following command: “pb_mpi -S -d supermatrix.dense.phylip -cat -gtr outputFile”. A total of 31,623 generations were run over three chains.
Download PhyloBayes.Results.Dense.tre (1.06 Kb)
Download README.txt (1.314 Kb)
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Title Species tree from RAxML analysis on dense supermatrix
Downloaded 9 times
Description Maximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the dense supermatrix using the GAMMAWAG model with 1,000 boot strap iterations.
Download RAxML.Results.Dense.tre (1.915 Kb)
Download README.txt (1.314 Kb)
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Title Species tree from RAxML analysis on sparse supermatrix
Downloaded 9 times
Description Maximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the sparse supermatrix using the GAMMAWAG model with 100 boot strap iterations.
Download RAxML.Results.Sparse.tre (1.917 Kb)
Download README.txt (1.314 Kb)
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Title SOWHAT constraint tree - Asteroidea and Echinozoa
Downloaded 7 times
Description The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop >output.txt”. This constraint tree was constructed to test if Asteroidea was a sister group to Echinozoa.
Download README.txt (1.314 Kb)
Download SOWHATconstraintTree-AsterSister2Echinozoa.tre (476 bytes)
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Title SOWHAT constraint tree - Crytosynirgid hypothesis
Downloaded 8 times
Description The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop >output.txt”. This constraint tree was constructed to test the Cryptosynirgid hypothesis.
Download SOWHATconstraintTree-Crytosynirgid.tre (476 bytes)
Download README.txt (1.314 Kb)
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Title SOWHAT constraint tree - Ophiuroidea and echinoderms
Downloaded 4 times
Description The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop >output.txt”. This constraint tree was constructed to test if Ophiuroidea was a sister group to the rest of echinoderms.
Download SOWHATconstraintTree-OphioSister2Echinoderms.tre (476 bytes)
Download README.txt (1.314 Kb)
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When using this data, please cite the original publication:

Reich A, Dunn C, Akasaka K, Wessel G (2015) Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. PLoS ONE 10(3): e0119627. http://dx.doi.org/10.1371/journal.pone.0119627

Additionally, please cite the Dryad data package:

Reich A, Dunn C, Akasaka K, Wessel G (2015) Data from: Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.22sf3
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