Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal

Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, Giribet G

Date Published: November 7, 2014

DOI: http://dx.doi.org/10.5061/dryad.nb2f7

 

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Title 3644-ortholog alignment
Downloaded 18 times
Description 3644-ortholog alignment of Arachnida, with 47 taxa
Download AL13_47.phy (85.21 Mb)
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Title Gene partitions file for 3644-ortholog alignment
Downloaded 13 times
Description Gene partitions file for 3644-ortholog alignment
Download AlignmentAL13.txt (129.3 Kb)
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Title 2806-ortholog alignment
Downloaded 9 times
Description 2806-ortholog alignment of Arachnida, with at least 15 taxa represented for each gene.
Download AL15.phy (67.41 Mb)
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Title Gene partitions file for 2806-ortholog alignment
Downloaded 3 times
Description Gene partitions file for 2806-ortholog alignment
Download AlignmentAL15.txt (98.16 Kb)
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Title 1152-ortholog alignment
Downloaded 10 times
Description 1152-ortholog alignment of Arachnida, with at least 20 taxa represented for each gene.
Download AL20.phy (23.51 Mb)
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Title Gene partitions file for 1152-ortholog alignment
Downloaded 2 times
Description Gene partitions file for 1152-ortholog alignment
Download AlignmentAL20.txt (39.84 Kb)
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Title 352-ortholog alignment
Downloaded 16 times
Description 352-ortholog alignment of Arachnida, with at least 25 taxa represented for each gene.
Download AL25.phy (3.799 Mb)
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Title Gene partitions file for 352-ortholog alignment
Downloaded 7 times
Description Gene partitions file for 352-ortholog alignment
Download AlignmentAL25.txt (12.08 Kb)
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Title 98-ortholog alignment
Downloaded 13 times
Description 98-ortholog alignment of Arachnida, with at least 30 taxa represented for each gene
Download AL30.phy (1.248 Mb)
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Title Gene partitions file for 98-ortholog alignment
Downloaded 3 times
Description Gene partitions file for 98-ortholog alignment
Download AlignmentAL30.txt (3.186 Kb)
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Title 23-ortholog alignment
Downloaded 23 times
Description 23-ortholog alignment of Arachnida, with at least 35 taxa represented for each gene.
Download AL35.phy (303.8 Kb)
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Title Gene partitions file for 23-ortholog alignment
Downloaded 4 times
Description Gene partitions file for 23-ortholog alignment
Download AlignmentAL35.txt (717 bytes)
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Title 516-ortholog alignment from MAtrix REduction (MARE)
Downloaded 6 times
Description 516-ortholog alignment from MAtrix REduction (MARE), retaining all 47 taxa
Download AL13MARE.phy (9.209 Mb)
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Title Gene partitions file for 516-ortholog MARE alignment
Downloaded 3 times
Description Gene partitions file for 516-ortholog MARE alignment
Download AlignmentMARE.txt (14.23 Kb)
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Title 1237-ortholog alignment from MAtrix REduction (MARE)
Downloaded 9 times
Description 1237-ortholog alignment with MAtrix REduction (MARE), retaining taxa with full genomes or Illumina libraries only
Download AL13MARE2.phy (15.68 Mb)
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Title Gene partitions file for 1237-ortholog MARE alignment
Downloaded 1 time
Description Gene partitions file for 1237-ortholog MARE alignment
Download AlignmentMARE2.txt (35.28 Kb)
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Title 3644-ortholog alignment with data-rich terminals only
Downloaded 11 times
Description 3644-ortholog alignment, retaining only terminals with full genomes or Illumina libraries
Download AL13_NGS.phy (51.92 Mb)
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Title 100 slowest-evolving orthologs alignment
Downloaded 22 times
Description 100-slowest-evolving orthologs alignment
Download G100.phy (2.136 Mb)
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Title Gene partitions file for 100 slowest-evolving orthologs
Downloaded 4 times
Description Gene partitions file for 100 slowest-evolving orthologs
Download AlignmentG100.txt (3.251 Kb)
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Title 200 slowest-evolving orthologs alignment
Downloaded 8 times
Description 200 slowest-evolving orthologs alignment
Download G200.phy (4.508 Mb)
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Title Gene partitions file for 200 slowest-evolving orthologs
Downloaded 5 times
Description Gene partitions file for 200 slowest-evolving orthologs
Download AlignmentG200.txt (6.589 Kb)
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Title 300 slowest-evolving orthologs alignment
Downloaded 10 times
Description 300 slowest-evolving orthologs alignment
Download G300.phy (7.281 Mb)
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Title Gene partitions file for 300 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 300 slowest-evolving orthologs
Download AlignmentG300.txt (9.911 Kb)
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Title 400 slowest-evolving orthologs alignment
Downloaded 5 times
Description 400 slowest-evolving orthologs alignment
Download G400.phy (10.03 Mb)
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Title Gene partitions file for 400 slowest-evolving orthologs
Downloaded 1 time
Description Gene partitions file for 400 slowest-evolving orthologs
Download AlignmentG400.txt (13.41 Kb)
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Title 500 slowest-evolving orthologs alignment
Downloaded 8 times
Description 500 slowest-evolving orthologs alignment
Download G500.phy (12.93 Mb)
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Title Gene partitions file for 500 slowest-evolving orthologs
Downloaded 3 times
Description Gene partitions file for 500 slowest-evolving orthologs
Download AlignmentG500.txt (16.92 Kb)
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Title 600 slowest-evolving orthologs alignment
Downloaded 12 times
Description 600 slowest-evolving orthologs alignment
Download G600.phy (15.94 Mb)
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Title Gene partitions file for 600 slowest-evolving orthologs
Downloaded 4 times
Description Gene partitions file for 600 slowest-evolving orthologs
Download AlignmentG600.txt (20.43 Kb)
Details View File Details
Title 700 slowest-evolving orthologs alignment
Downloaded 4 times
Description 700 slowest-evolving orthologs alignment
Download G700.phy (18.69 Mb)
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Title Gene partitions file for 700 slowest-evolving orthologs
Downloaded 1 time
Description Gene partitions file for 700 slowest-evolving orthologs
Download AlignmentG700.txt (23.96 Kb)
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Title 800 slowest-evolving orthologs alignment
Downloaded 10 times
Description 800 slowest-evolving orthologs alignment
Download G800.phy (21.83 Mb)
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Title Gene partitions file for 800 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 800 slowest-evolving orthologs
Download AlignmentG800.txt (27.47 Kb)
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Title 900 slowest-evolving orthologs alignment
Downloaded 6 times
Description 900 slowest-evolving orthologs alignment
Download G900.phy (24.64 Mb)
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Title Gene partitions file for 900 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 900 slowest-evolving orthologs
Download AlignmentG900.txt (30.98 Kb)
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Title 1000 slowest-evolving orthologs alignment
Downloaded 9 times
Description 1000 slowest-evolving orthologs alignment
Download G1000.phy (27.46 Mb)
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Title Gene partitions file for 1000 slowest-evolving orthologs
Downloaded 2 times
Download AlignmentG1000.txt (34.50 Kb)
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Title 1500 slowest-evolving orthologs alignment
Downloaded 8 times
Description 1500 slowest-evolving orthologs alignment
Download G1500.phy (41.60 Mb)
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Title Gene partitions file for 1500 slowest-evolving orthologs
Downloaded 3 times
Description Gene partitions file for 1500 slowest-evolving orthologs
Download AlignmentG1500.txt (52.08 Kb)
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Title 2000 slowest-evolving orthologs alignment
Downloaded 4 times
Description 2000 slowest-evolving orthologs alignment
Download G2000.phy (54.90 Mb)
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Title Gene partitions file for 2000 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 2000 slowest-evolving orthologs
Download AlignmentG2000.txt (69.71 Kb)
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Title 2500 slowest-evolving orthologs alignment
Downloaded 6 times
Description 2500 slowest-evolving orthologs alignment
Download G2500.phy (67.42 Mb)
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Title 3000 slowest-evolving orthologs alignment
Downloaded 8 times
Description 3000 slowest-evolving orthologs alignment
Download G3000.phy (79.36 Mb)
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Title Gene partitions file for 2500 slowest-evolving orthologs
Downloaded 3 times
Description Gene partitions file for 2500 slowest-evolving orthologs
Download AlignmentG2500.txt (87.36 Kb)
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Title Gene partitions file for 3000 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 3000 slowest-evolving orthologs
Download AlignmentG3000.txt (105.4 Kb)
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Title 3500 slowest-evolving orthologs alignment
Downloaded 9 times
Description 3500 slowest-evolving orthologs alignment
Download G3500.phy (90.19 Mb)
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Title Gene partitions file for 3500 slowest-evolving orthologs
Downloaded 2 times
Description Gene partitions file for 3500 slowest-evolving orthologs
Download AlignmentG3500.txt (124.1 Kb)
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Title Alipes grandidieri Trinity assembly
Downloaded 11 times
Description Alipes grandidieri (Chilopoda: Scolopendromorpha) Trinity assembly
Download Alipes.fasta (87.74 Mb)
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Title Centruroides vittatus Trinity assembly
Downloaded 10 times
Description Centruroides vittatus (Chelicerata: Scorpiones) Trinity assembly
Download Centruroides.fasta (6.159 Mb)
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Title Damon variegatus Trinity assembly
Downloaded 9 times
Description Damon variegatus (Chelicerata: Amblypygi) Trinity assembly
Download Damon.fasta (38.05 Mb)
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Title Eremobates sp. Trinity assembly
Downloaded 9 times
Description Eremobates sp. (Chelicerata: Solifugae) Trinity assembly
Download Eremobates.fasta (60.61 Mb)
Details View File Details
Title Frontinella communis Trinity assembly
Downloaded 12 times
Description Frontinella communes (Chelicerata: Araneae) Trinity assembly
Download Frontinella.fasta (125.7 Mb)
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Title Hesperonemastoma modestum Trinity assembly
Downloaded 13 times
Description Hesperonemastoma modestum (Chelicerata: Opiliones) Trinity assembly
Download Hesperonemastoma.fasta (73.50 Mb)
Details View File Details
Title Larifuga capensis Trinity assembly
Downloaded 11 times
Description Larifuga capensis (Chelicerata: Opiliones) Trinity assembly
Download Larifuga.fasta (74.21 Mb)
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Title Leiobunum verrucosum Trinity assembly
Downloaded 9 times
Description Leiobunum verrucosum (Chelicerata: Opiliones) Trinity assembly
Download Leiobunum.fasta (62.25 Mb)
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Title Leucage venusta Trinity assembly
Downloaded 11 times
Description Leucage venusta (Chelicerata: Opiliones) Trinity assembly
Download Leucage.fasta (171.6 Mb)
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Title Limulus polyphemus Trinity assembly
Downloaded 10 times
Description Limulus polyphemus (Chelicerata: Xiphosura) Trinity assembly
Download Limulus.fasta (96.32 Mb)
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Title Liphistius malayanus Trinity assembly
Downloaded 15 times
Description Liphistius malayanus (Chelicerata: Araneae) Trinity assembly
Download Liphistius.fasta (40.53 Mb)
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Title Mastigoproctus giganteus Trinity assembly
Downloaded 8 times
Description Mastigoproctus giantess (Chelicerata: Uropygi) Trinity assembly
Download Mastigoproctus.fasta (80.19 Mb)
Details View File Details
Title Metabiantes sp. Trinity assembly
Downloaded 10 times
Description Metabiantes sp. (Chelicerata: Opiliones) Trinity assembly
Download Metabiantes.fasta (106.0 Mb)
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Title Metasiro americanus Trinity assembly
Downloaded 8 times
Description Metasiro americanus (Chelicerata: Opiliones) Trinity assembly
Download Metasiro.fasta (55.69 Mb)
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Title Neoscona arabesca Trinity assembly
Downloaded 11 times
Description Neoscona arabesca (Chelicerata: Araneae) Trinity assembly
Download Neoscona.fasta (117.9 Mb)
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Title Ortholasma coronadense Trinity assembly
Downloaded 7 times
Description Ortholasma corona dense (Chelicerata: Opiliones) Trinity assembly
Download Ortho.fasta (76.13 Mb)
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Title Pachylicus acutus Trinity assembly
Downloaded 9 times
Description Pachylicus acutus (Chelicerata: Opiliones) Trinity assembly
Download Pachylicus.fasta (56.64 Mb)
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Title Peripatopsis capensis Trinity assembly
Downloaded 11 times
Description Peripatopsis capensis (Onychophora: Peripatopsidae) Trinity assembly
Download Peripatopsis2.fasta (46.67 Mb)
Details View File Details
Title Phalangium opilio Trinity assembly
Downloaded 10 times
Description Phalangium opilio (Chelicerata: Opiliones) Trinity assembly
Download Phalangium.fasta (97.71 Mb)
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Title Protolophus singularis Trinity assembly
Downloaded 8 times
Description Protolophus singulars (Chelicerata: Opiliones) Trinity assembly
Download Protolophus.fasta (239.8 Mb)
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Title Pseudocellus sp. Trinity assembly
Downloaded 13 times
Description Pseudocellus sp. (Chelicerata: Ricinulei) Trinity assembly
Download Pseudocellus.fasta (14.52 Mb)
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Title Sclerobunus nondimorphicus Trinity assembly
Downloaded 10 times
Description Sclerobunus nondimorphicus (Chelicerata: Opiliones) Trinity assembly
Download Sclerobunus.fasta (86.40 Mb)
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Title Ricinoides atewa Trinity assembly
Downloaded 11 times
Description Ricinoides atewa (Chelicerata: Ricinulei) Trinity assembly
Download Ricinoides.fasta (67.62 Mb)
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Title Siro boyerae Trinity assembly
Downloaded 8 times
Description Siro boyerae (Chelicerata: Opiliones) Trinity assembly
Download Siro.fasta (38.41 Mb)
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Title Sitalcina lobata Trinity assembly
Downloaded 14 times
Description Sitalcina lobata (Chelicerata: Opiliones) Trinity assembly
Download Sitalcina.fasta (80.12 Mb)
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Title Synsphyronus apimelus Trinity assembly
Downloaded 11 times
Description Synsphyronus apimelus (Chelicerata: Pseudoscorpiones) Trinity assembly
Download Synsphyronus.fasta (80.61 Mb)
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Title Trogulus martensi Trinity assembly
Downloaded 9 times
Description Trogulus martensi (Chelicerata: Opiliones) Trinity assembly
Download Trogulus.fasta (67.55 Mb)
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Title Vonones ornata Trinity assembly
Downloaded 12 times
Description Vonones ornate (Chelicerata: Opiliones) Trinity assembly
Download Vonones.fasta (121.0 Mb)
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When using this data, please cite the original publication:

Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, Giribet G (2014) Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal. Molecular Biology and Evolution 31(11): 2963-2984. http://dx.doi.org/10.1093/molbev/msu235

Additionally, please cite the Dryad data package:

Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, Giribet G (2014) Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nb2f7
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