Datasets

SATe experiment simulated nucleotide datasets README

There are 37 model conditions, with either 1000, 500, or 100 taxa, and either long, medium, or short gap length types. Each model condition is referred to with the string "<number of taxa><gap length type: L for long, M for medium, S for short><id number>".
Each model condition has 20 replicate datasets.
For each model condition, an associated link to a tarball is listed below. The tarball contains the 20 replicate datasets for that model condition.
After decompressing a tarball, the directory structure ./R<replicate number>/ will have the following files:

rose.tt - Potentiall Inferrable Model Tree, or PIMT, (model tree with zero event edges collapsed) in Newick format
rose.mt - binary model tree in Newick format
rose.aln.true.fasta - true alignment in FASTA format
rose.mt.internal - binary model tree with all nodes named in Newick format
rose.aln.true.internal.fasta - true alignment for all nodes' sequences in FASTA format

1000 long	1000 medium	1000 short	500 long	500 medium	500 short	100 long	100 medium	100 short
1000L1 1000L2 1000L3 1000L4 1000L5	1000M1 1000M2 1000M3 1000M4 1000M5	1000S1 1000S2 1000S3 1000S4 1000S5	500L1 500L2 500L3 500L4 500L5	500M1 500M2 500M3 500M4 500M5	500S1 500S2 500S3 500S4 500S5	100L1 100L2	100M1 100M2 100M3	100S1 100S2

These model conditions have the following empirical statistics.

True Alignment Statistics (Set-wise)
PIMT Statistics
(Branch-wise)
PIMT Statistics

Model Avg p-dist
Max p-dist
% indels
No. of cols
Avg gap len Median gap len e-ANHD e-gap True tree percent reso

1000L1 69.5% 76.9% 73.2% 3817.5 13.6 10.7 25.3% 0.2% 99.7%

1000L2 69.6% 76.9% 57.7% 2406.9 11.6 9.3 25.1% 0.1% 99.6%

1000L3 68.7% 76.3% 85.2% 7042.8 20.0 16.1 22.8% 0.3% 99.7%

1000L4 50.0% 60.8% 58.6% 2446.2 11.4 9.2 6.5% 0.1% 97.6%

1000L5 49.6% 60.6% 42.6% 1764.8 10.4 8.0 6.5% 0.0% 97.4%

1000M1 69.5% 76.9% 74.4% 3965.0 10.1 8.0 24.8% 0.2% 99.6%

1000M2 68.4% 76.2% 74.2% 3972.3 10.3 7.9 22.1% 0.2% 99.5%

1000M3 66.0% 74.1% 62.8% 2722.6 7.6 5.6 18.0% 0.1% 99.4%

1000M4 49.5% 60.6% 60.5% 2570.6 7.6 5.8 6.6% 0.1% 97.6%

1000M5 49.9% 60.2% 44.2% 1810.0 6.2 4.4 6.8% 0.1% 97.8%

1000S1 69.4% 76.8% 53.0% 2141.2 4.0 3.4 24.5% 0.1% 99.7%

1000S2 69.3% 76.8% 35.0% 1546.0 2.9 2.4 23.8% 0.0% 99.7%

1000S3 68.6% 76.3% 37.0% 1595.2 2.9 2.4 22.3% 0.0% 99.6%

1000S4 50.1% 60.8% 24.6% 1328.1 2.5 2.0 6.7% 0.0% 97.9%

1000S5 49.8% 61.1% 14.1% 1165.2 2.3 2.0 6.5% 0.0% 97.8%

500L1 67.0% 74.9% 80.5% 5419.3 17.0 13.0 21.2% 0.5% 99.5%

500L2 65.7% 73.9% 80.9% 5475.9 16.9 12.7 19.3% 0.5% 99.4%

500L3 65.8% 74.1% 68.6% 3306.9 12.9 10.3 19.4% 0.3% 99.4%

500L4 49.9% 60.7% 69.6% 3390.2 13.3 10.0 7.5% 0.3% 98.3%

500L5 49.7% 60.6% 51.0% 2075.3 10.9 8.6 7.1% 0.1% 97.8%

500M1 67.4% 74.8% 70.9% 3522.3 9.1 6.8 22.7% 0.3% 99.5%

500M2 65.8% 74.0% 69.7% 3394.5 9.0 6.5 19.4% 0.3% 99.5%

500M3 65.7% 73.7% 53.5% 2185.2 6.8 4.9 19.4% 0.2% 99.4%

500M4 49.1% 60.5% 52.5% 2154.6 6.7 4.9 7.0% 0.1% 98.0%

500M5 49.5% 60.5% 35.6% 1568.2 5.7 4.2 7.3% 0.1% 98.1%

500S1 67.3% 75.2% 48.7% 1962.2 3.6 3.0 22.2% 0.2% 99.5%

500S2 65.5% 73.7% 48.0% 1935.8 3.6 2.9 19.1% 0.2% 99.5%

500S3 65.6% 73.6% 31.7% 1468.2 2.7 2.0 19.4% 0.1% 99.5%

500S4 49.2% 60.6% 31.3% 1459.8 2.7 2.0 7.2% 0.1% 98.2%

500S5 49.8% 60.4% 18.7% 1231.0 2.3 1.9 7.3% 0.0% 98.0%

100L1 62.3% 71.0% 56.4% 2459.7 11.2 8.1 20.5% 0.8% 99.7%

100L2 32.2% 44.4% 53.6% 2281.9 11.4 8.5 4.3% 0.7% 95.9%

100M1 62.6% 71.0% 55.1% 2316.8 7.1 4.8 20.4% 0.8% 99.7%

100M2 53.1% 63.3% 53.6% 2262.9 7.0 4.8 12.7% 0.8% 99.3%

100M3 45.0% 56.4% 38.9% 1681.9 5.9 4.2 8.1% 0.4% 98.4%

100S1 58.0% 67.5% 40.4% 1698.2 3.1 2.6 16.1% 0.6% 99.0%

100S2 32.0% 43.6% 57.2% 2418.3 4.6 3.6 4.6% 1.1% 96.8%

Main biological DNA/RNA datasets README

There are 171 biological datasets. Each dataset consists of either DNA or RNA sequences from a variety of markers and taxa.
For each dataset, an associated link to a tarball is listed below. The tarball contains a single directory ./R0/ that contains the following files:

cleaned.alignment.fasta - cleaned curated alignment in FASTA format
cleaned.alignment.fasta.name_map - bijective mapping between original taxon names and cleaned taxon names in columnar format

rRNA datasets	tRNA datasets	Intronic datasets	Avian datasets	Miscellaneous
16S.A.ALL 16S.A.aa_ag 16S.A.crenarchaeota 16S.A.euryarchaeota 16S.B.aquificae 16S.B.bacteroidetes-chlorobi 16S.B.chlamydiae-verrucomicrobia 16S.B.chloroflexi 16S.B.clostridia 16S.B.cyanobacteria 16S.B.deinococcus-thermus 16S.B.delta-epsilon-proteobacteria 16S.B.fibrobacteres-acidiobacteria 16S.B.fusobacteria 16S.B.mollicutes 16S.B.nitrospirae 16S.B.planctomycetes 16S.B.spirochaetes 16S.B.thermotogae 16S.C.aa_ag 16S.C 16S.E.aa_ag 16S.E.acanthamoeba 16S.E.bacillariophyta 16S.E.blastocystis 16S.E.coccidia 16S.E.entamoebidae 16S.E.giardiinae 16S.E.haemosporida 16S.E.haplosporida 16S.E.heterolobosea 16S.E.litostomatea 16S.E.lobosea 16S.E.oomycetes 16S.E.parabasalidea 16S.E.perkinsea 16S.E.piroplasmida 16S.E.trypanosomatidae 16S.M.aa_ag 16S.M 16S.fungint.all 16S.fungint.nint 16S.fungint.wint 23S.3 23S.A.aa_ag 23S.A 23S.B.aa_ag 23S.B.gammaproteobacteria 23S.B.proteobacteria 23S.C.aa_ag 23S.C 23S.E.aa_ag 23S.E 23S.M.aa_ag 23S.M 23S.fungint.all 23S.fungint.nint 5S.3 5S.A 5S.B.ALL 5S.B.actinobacteria 5S.B.alphaproteobacteria 5S.B.bacillusclostridium 5S.B.betaproteobacteria 5S.B.firmicutes 5S.B.gammaproteobacteria 5S.B.proteobacteria 5S.C 5S.E 5S.M 5S.T seed.16S.A seed.16S.B seed.23S.A	trna.A.nm trna.C.nm trna.D.nm trna.E.nm trna.F.nm trna.G.nm trna.H.nm trna.I.nm trna.K.nm trna.M.nm trna.N.nm trna.P.nm trna.Q.nm trna.W.nm trna.Y1.nm	I1.A I1.B I1.C1 I1.C2 I1.C3 I1.D I1.E I2.A I2.B	avian_ACA_all avian_ACA_intron1 avian_ALD_all avian_ALD_intron3 avian_ALD_intron4 avian_ALD_intron5 avian_ALD_intron6 avian_ALD_intron7 avian_BDNF_all avian_CHC_all avian_CHC_intron4 avian_CHC_intron5 avian_CMYC_UTR avian_CMYC_all avian_CMYC_intronB avian_DCOH_all avian_DCOH_intron2 avian_DCOH_intron3 avian_EEF_all avian_EEF_intron4 avian_EEF_intron5 avian_EEF_intron6 avian_EEF_intron7 avian_EGR1_UTR avian_EGR1_all avian_EXONS_ALL avian_FIB4_all avian_FIB4_intron4 avian_FIB5_all avian_FIB5_intron5 avian_FIB67_all avian_FIB67_intron6 avian_FIB67_intron7 avian_FIB_all avian_HMG_all avian_HMG_intron2 avian_HMG_intron3 avian_HMG_intron4 avian_HMG_intron5 avian_IRF2_all avian_IRF2_intron2 avian_MUSK_all avian_MUSK_intron4 avian_MYO_all avian_MYO_intron2 avian_NGF_UTR avian_NGF_all avian_NT3_all avian_RHOD_all avian_RHOD_intron1 avian_RHOD_intron2 avian_RHOD_intron3 avian_SOMA_all avian_SOMA_intron2 avian_SOMA_intron3 avian_TGF_all avian_TGF_intron5 avian_TROP_all avian_TROP_intron6 avian_UTRS_ALL	Aster_ITS E_hildenbrandia diatom linder_asteraceae linder_helianthus_104 linder_helianthus_actin mollusk_mito moody_halorag morrison_coccidia rhodstram.18S rhodstram.intron theriot_diatom_ssu theriot_heterokont_ssu

Largest biological RNA datasets README

There are 171 biological datasets. Each dataset consists of RNA sequences from a variety of markers and taxa.
For each dataset, an associated link to a tarball is listed below. The tarball contains a single directory ./R0/ that contains the following files:

cleaned.alignment.fasta - cleaned curated alignment in FASTA format
cleaned.alignment.fasta.name_map - bijective mapping between original taxon names and cleaned taxon names in columnar format

16S.3
16S.B.ALL
16S.B.aa_ag
16S.B.actinobacteria
16S.B.alphaproteobacteria
16S.B.bacilli
16S.B.betaproteobacteria
16S.B.firmicutes
16S.B.gammaproteobacteria
16S.B.proteobacteria
16S.E.ALL
16S.E.streptophyta
16S.T
23S.B.ALL
23S.T
seed.23S.B

Two-phase experiment simulated DNA datasets README

There are 84 model conditions, with either 1000, 500, or 100 taxa, and either long, medium, or short gap length types. Each model condition is referred to with the string "<number of taxa><gap length type: L for long, M for medium, S for short>-<id number>".
Each model condition has 20 replicate datasets.
For each model condition, an associated link to a tarball is listed below. The tarball contains the 20 replicate datasets for that model condition.
After decompressing a tarball, the directory structure ./R<replicate number>/ will have the following files:

TODO

1000 long	1000 medium	1000 short	500 long	500 medium	500 short	100 long	100 medium	100 short
1000L-1 1000L-2 1000L-3 1000L-4 1000L-5 1000L-6 1000L-7 1000L-8 1000L-9 1000L-10	1000M-1 1000M-2 1000M-3 1000M-4 1000M-5 1000M-6 1000M-7 1000M-8	1000S-1 1000S-2 1000S-3 1000S-4 1000S-5 1000S-6 1000S-7 1000S-8 1000S-9 1000S-10	500L-1 500L-2 500L-3 500L-4 500L-5 500L-6 500L-7 500L-8 500L-9 500L-10	500M-1 500M-2 500M-3 500M-4 500M-5 500M-6 500M-7 500M-8	500S-1 500S-2 500S-3 500S-4 500S-5 500S-6 500S-7 500S-8 500S-9 500S-10	100L-1 100L-2 100L-3 100L-4 100L-5 100L-6 100L-7 100L-8 100L-9 100L-10	100M-1 100M-2 100M-3 100M-4 100M-5 100M-6 100M-7 100M-8	100S-1 100S-2 100S-3 100S-4 100S-5 100S-6 100S-7 100S-8 100S-9 100S-10

	True Alignment Statistics (Set-wise)						PIMT Statistics (Branch-wise)		PIMT Statistics
Model	Avg p-dist	Max p-dist	% indels	No. of cols	Avg gap len	Median gap len	e-ANHD	e-gap	True tree percent reso
1000L1	69.5%	76.9%	73.2%	3817.5	13.6	10.7	25.3%	0.2%	99.7%
1000L2	69.6%	76.9%	57.7%	2406.9	11.6	9.3	25.1%	0.1%	99.6%
1000L3	68.7%	76.3%	85.2%	7042.8	20.0	16.1	22.8%	0.3%	99.7%
1000L4	50.0%	60.8%	58.6%	2446.2	11.4	9.2	6.5%	0.1%	97.6%
1000L5	49.6%	60.6%	42.6%	1764.8	10.4	8.0	6.5%	0.0%	97.4%
1000M1	69.5%	76.9%	74.4%	3965.0	10.1	8.0	24.8%	0.2%	99.6%
1000M2	68.4%	76.2%	74.2%	3972.3	10.3	7.9	22.1%	0.2%	99.5%
1000M3	66.0%	74.1%	62.8%	2722.6	7.6	5.6	18.0%	0.1%	99.4%
1000M4	49.5%	60.6%	60.5%	2570.6	7.6	5.8	6.6%	0.1%	97.6%
1000M5	49.9%	60.2%	44.2%	1810.0	6.2	4.4	6.8%	0.1%	97.8%
1000S1	69.4%	76.8%	53.0%	2141.2	4.0	3.4	24.5%	0.1%	99.7%
1000S2	69.3%	76.8%	35.0%	1546.0	2.9	2.4	23.8%	0.0%	99.7%
1000S3	68.6%	76.3%	37.0%	1595.2	2.9	2.4	22.3%	0.0%	99.6%
1000S4	50.1%	60.8%	24.6%	1328.1	2.5	2.0	6.7%	0.0%	97.9%
1000S5	49.8%	61.1%	14.1%	1165.2	2.3	2.0	6.5%	0.0%	97.8%
500L1	67.0%	74.9%	80.5%	5419.3	17.0	13.0	21.2%	0.5%	99.5%
500L2	65.7%	73.9%	80.9%	5475.9	16.9	12.7	19.3%	0.5%	99.4%
500L3	65.8%	74.1%	68.6%	3306.9	12.9	10.3	19.4%	0.3%	99.4%
500L4	49.9%	60.7%	69.6%	3390.2	13.3	10.0	7.5%	0.3%	98.3%
500L5	49.7%	60.6%	51.0%	2075.3	10.9	8.6	7.1%	0.1%	97.8%
500M1	67.4%	74.8%	70.9%	3522.3	9.1	6.8	22.7%	0.3%	99.5%
500M2	65.8%	74.0%	69.7%	3394.5	9.0	6.5	19.4%	0.3%	99.5%
500M3	65.7%	73.7%	53.5%	2185.2	6.8	4.9	19.4%	0.2%	99.4%
500M4	49.1%	60.5%	52.5%	2154.6	6.7	4.9	7.0%	0.1%	98.0%
500M5	49.5%	60.5%	35.6%	1568.2	5.7	4.2	7.3%	0.1%	98.1%
500S1	67.3%	75.2%	48.7%	1962.2	3.6	3.0	22.2%	0.2%	99.5%
500S2	65.5%	73.7%	48.0%	1935.8	3.6	2.9	19.1%	0.2%	99.5%
500S3	65.6%	73.6%	31.7%	1468.2	2.7	2.0	19.4%	0.1%	99.5%
500S4	49.2%	60.6%	31.3%	1459.8	2.7	2.0	7.2%	0.1%	98.2%
500S5	49.8%	60.4%	18.7%	1231.0	2.3	1.9	7.3%	0.0%	98.0%
100L1	62.3%	71.0%	56.4%	2459.7	11.2	8.1	20.5%	0.8%	99.7%
100L2	32.2%	44.4%	53.6%	2281.9	11.4	8.5	4.3%	0.7%	95.9%
100M1	62.6%	71.0%	55.1%	2316.8	7.1	4.8	20.4%	0.8%	99.7%
100M2	53.1%	63.3%	53.6%	2262.9	7.0	4.8	12.7%	0.8%	99.3%
100M3	45.0%	56.4%	38.9%	1681.9	5.9	4.2	8.1%	0.4%	98.4%
100S1	58.0%	67.5%	40.4%	1698.2	3.1	2.6	16.1%	0.6%	99.0%
100S2	32.0%	43.6%	57.2%	2418.3	4.6	3.6	4.6%	1.1%	96.8%