Full-taxa Phylip file: allTaxa.c85d6m20p3.2016.12.08.phy

Phylogeny Result

Won Kim (6426446)

March 2019

This fileset contains following contents;BUSCO_single_copy_gene_tree.zip: a supermatrix aln.faa file...

Full nuclear phylogenomic analysis -- best tree with bipartition frequencies

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

Phylogeny file

Chris Klingenberg (3286884)
Jesús Marugán-Lobón (153200)

October 2016

Nexus file with the phylogeny used in the analysis. This tree was constructed using the tree of Hack...

Loci file from pyRAD: c85d6m20p3.full.loci

Andrew L. Hipp (508078)
Paul S. Manos (547688)
Antonio Gonzalez-Rodriguez (5026961)
Marlene Hahn (3196947)
Matthew Kaproth (5026958)
John D. McVay (3965336)
Susana Valencia Avalos (5026964)
Jeannine Cavender-Bares (263456)

March 2018

Loci file exported from clustering analysis performed in PyRAD. All molecular datasets referenced in...

Phylo6_247_April2012

David Luke Field (3243849)
Melinda Pickup (3243846)
Spencer C. H. Barrett (94488)

October 2016

Original nexus file containing the phylogenetic data. This is not the final data analysed as it cont...

Full nuclear phylogenomic analysis -- bootstrap trees

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

phylogenetic-analysis-steps.txt

McGee, Matthew D.
Faircloth, Brant C.
Borstein, Samuel R.
Zheng, Jimmy
Hulsey, Christopher Darrin
Wainwright, Peter C.
Alfaro, Michael E.

January 2016

Steps used during the phylogenetic analysis. All used the PHYLUCE software package (available from:...

Full nuclear phylogenomic analysis -- concatenated alignment

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

PhyloSift: phylogenetic analysis of genomes and metagenomes (supplementary manuscript data)

Holly Bik (384795)
Jonathan Eisen (97599)
Erick Matsen (385742)
Eric Lowe (385741)
Guillaume Jospin (385740)
Aaron Darling (61404)

March 2013

These files are supplementary data for the following manuscript: Darling AE, Jospi...

Whole-genome SNP phylogeny (restricted dataset), related to Figure S3

Almeida, Pedro
Barbosa, Raquel
Zalar, Polona
Imanishi, Yumi
Shimizu, Kiminori
Turchetti, Benedetta
Legras, Jean-Luc
Serra, Marta
Dequin, Sylvie
Couloux, Arnaud
Guy, Julie
Bensasson, Douda
Gonçalves, Paula
Sampaio, José Paulo

August 2015

RAxML phylogenetic tree in newick format, obtained from the whole-genome SNP alignment of the restri...

Phylogenetic Analyses

Kieren J. Mitchell (3262926)
Bastien Llamas (187276)
Julien Soubrier (198167)
Nicolas J. Rawlence (154484)
Trevor W. Worthy (3326865)
Jamie Wood (3326844)
Michael S. Y. Lee (2583253)
Alan Cooper (9827)

November 2016

Input-files (data) and resulting phylogenetic tree(s) for all RAxML, MrBayes, PAUP* and BEAST analys...

Whole-genome SNP phylogeny (restricted dataset), related to Figure 3

Almeida, Pedro
Barbosa, Raquel
Zalar, Polona
Imanishi, Yumi
Shimizu, Kiminori
Turchetti, Benedetta
Legras, Jean-Luc
Serra, Marta
Dequin, Sylvie
Couloux, Arnaud
Guy, Julie
Bensasson, Douda
Gonçalves, Paula
Sampaio, José Paulo

August 2015

RAxML phylogenetic tree obtained from the whole-genome SNP alignment of the restricted dataset and w...

UCE_phylip

Campillo, Luke C.
Oliveros, Carl H.
Sheldon, Frederick H.
Moyle, Robert G.

December 2017

This directory contains a phylip file for each locus in the complete UCE data matrix (n = 2,107 UCE ...

Haplotypes for all loci and individuals

Ebel, Emily R.
DaCosta, Jeffrey M.
Sorenson, Michael D.
Hill, Ryan I.
Briscoe, Adriana D.
Willmott, Keith R.
Mullen, Sean P.

March 2015

Output of the final step of the pyRAD software pipeline (Eaton and Ree, 2013). File contains both ha...

Complete RAD dataset in phylip format (zipped).

John D. McVay (3965336)
Andrew L. Hipp (508078)
Paul S. Manos (547688)

March 2018

Complete concatenated phylogenetic dataset ( min. 4 individuals per locus) in phylip format. Cluster...

Phylogeny Result

Won Kim (6426446)

March 2019

This fileset contains following contents;BUSCO_single_copy_gene_tree.zip: a supermatrix aln.faa file...

Full nuclear phylogenomic analysis -- best tree with bipartition frequencies

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

Phylogeny file

Chris Klingenberg (3286884)
Jesús Marugán-Lobón (153200)

October 2016

Nexus file with the phylogeny used in the analysis. This tree was constructed using the tree of Hack...

Loci file from pyRAD: c85d6m20p3.full.loci

Andrew L. Hipp (508078)
Paul S. Manos (547688)
Antonio Gonzalez-Rodriguez (5026961)
Marlene Hahn (3196947)
Matthew Kaproth (5026958)
John D. McVay (3965336)
Susana Valencia Avalos (5026964)
Jeannine Cavender-Bares (263456)

March 2018

Loci file exported from clustering analysis performed in PyRAD. All molecular datasets referenced in...

Phylo6_247_April2012

David Luke Field (3243849)
Melinda Pickup (3243846)
Spencer C. H. Barrett (94488)

October 2016

Original nexus file containing the phylogenetic data. This is not the final data analysed as it cont...

Full nuclear phylogenomic analysis -- bootstrap trees

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

phylogenetic-analysis-steps.txt

McGee, Matthew D.
Faircloth, Brant C.
Borstein, Samuel R.
Zheng, Jimmy
Hulsey, Christopher Darrin
Wainwright, Peter C.
Alfaro, Michael E.

January 2016

Steps used during the phylogenetic analysis. All used the PHYLUCE software package (available from:...

Full nuclear phylogenomic analysis -- concatenated alignment

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

PhyloSift: phylogenetic analysis of genomes and metagenomes (supplementary manuscript data)

Holly Bik (384795)
Jonathan Eisen (97599)
Erick Matsen (385742)
Eric Lowe (385741)
Guillaume Jospin (385740)
Aaron Darling (61404)

March 2013

These files are supplementary data for the following manuscript: Darling AE, Jospi...

Whole-genome SNP phylogeny (restricted dataset), related to Figure S3

Almeida, Pedro
Barbosa, Raquel
Zalar, Polona
Imanishi, Yumi
Shimizu, Kiminori
Turchetti, Benedetta
Legras, Jean-Luc
Serra, Marta
Dequin, Sylvie
Couloux, Arnaud
Guy, Julie
Bensasson, Douda
Gonçalves, Paula
Sampaio, José Paulo

August 2015

RAxML phylogenetic tree in newick format, obtained from the whole-genome SNP alignment of the restri...

Phylogenetic Analyses

Kieren J. Mitchell (3262926)
Bastien Llamas (187276)
Julien Soubrier (198167)
Nicolas J. Rawlence (154484)
Trevor W. Worthy (3326865)
Jamie Wood (3326844)
Michael S. Y. Lee (2583253)
Alan Cooper (9827)

November 2016

Input-files (data) and resulting phylogenetic tree(s) for all RAxML, MrBayes, PAUP* and BEAST analys...

Whole-genome SNP phylogeny (restricted dataset), related to Figure 3

Almeida, Pedro
Barbosa, Raquel
Zalar, Polona
Imanishi, Yumi
Shimizu, Kiminori
Turchetti, Benedetta
Legras, Jean-Luc
Serra, Marta
Dequin, Sylvie
Couloux, Arnaud
Guy, Julie
Bensasson, Douda
Gonçalves, Paula
Sampaio, José Paulo

August 2015

RAxML phylogenetic tree obtained from the whole-genome SNP alignment of the restricted dataset and w...

UCE_phylip

Campillo, Luke C.
Oliveros, Carl H.
Sheldon, Frederick H.
Moyle, Robert G.

December 2017

This directory contains a phylip file for each locus in the complete UCE data matrix (n = 2,107 UCE ...

Haplotypes for all loci and individuals

Ebel, Emily R.
DaCosta, Jeffrey M.
Sorenson, Michael D.
Hill, Ryan I.
Briscoe, Adriana D.
Willmott, Keith R.
Mullen, Sean P.

March 2015

Output of the final step of the pyRAD software pipeline (Eaton and Ree, 2013). File contains both ha...

Complete RAD dataset in phylip format (zipped).

John D. McVay (3965336)
Andrew L. Hipp (508078)
Paul S. Manos (547688)

March 2018

Complete concatenated phylogenetic dataset ( min. 4 individuals per locus) in phylip format. Cluster...

Phylogeny Result

Won Kim (6426446)

March 2019

This fileset contains following contents;BUSCO_single_copy_gene_tree.zip: a supermatrix aln.faa file...

Full nuclear phylogenomic analysis -- best tree with bipartition frequencies

Folk, Ryan A.
Visger, Clayton J
Soltis, Pamela Sue
Soltis, Douglas Edward
Guralnick, Robert Penn

March 2018

Analysis of all taxa (i.e., in some cases multiple accessions per species), from which a pruned one-...

Phylogeny file

Chris Klingenberg (3286884)
Jesús Marugán-Lobón (153200)

October 2016

Nexus file with the phylogeny used in the analysis. This tree was constructed using the tree of Hack...

Full-taxa Phylip file: allTaxa.c85d6m20p3.2016.12.08.phy

Abstract

Extracted data

Full-taxa Phylip file: allTaxa.c85d6m20p3.2016.12.08.phy

Abstract

Extracted data

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