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Datasets:
plantcad
/
andropogoneae_msa

Tags:
biology
genomics
dna
License:
Dataset card Files
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Files changed (8) hide show
  1. .gitattributes +2 -0
  2. README.md +13 -0
  3. msa.tar.gz +3 -0
  4. phastCons.bw +3 -0
  5. phyloP.bw +3 -0
  6. species.txt +36 -0
  7. species_metadata.tsv +37 -0
  8. tree.nh +1 -0
.gitattributes CHANGED
@@ -57,3 +57,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
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+ phyloP.bw filter=lfs diff=lfs merge=lfs -text
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+ phastCons.bw filter=lfs diff=lfs merge=lfs -text
README.md ADDED
@@ -0,0 +1,13 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ ---
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+ license: mit
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+ tags:
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+ - biology
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+ - genomics
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+ - dna
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+ ---
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+ # Andropogoneae MSA
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+
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+ `msa.tar.gz` was compressed with `pigz`. To uncompress using all cores:
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+ ```bash
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+ unpigz < msa.tar.gz | tar -x
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+ ```
msa.tar.gz ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:159ea206426bbff68f6b11ab51663c586908766df88f7ee863b613538a23bb4d
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+ size 3230672742
phastCons.bw ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:c0e86f90bd2d0cec22cc30f808922249d555f746f0dd06ad1042e530a8e922d0
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+ size 1133313404
phyloP.bw ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:be978f95b798bce163ce3568569a939c2dae2a9689e4a1b45b3b515f89a40651
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+ size 817540972
species.txt ADDED
@@ -0,0 +1,36 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ zB73v5
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+ zTIL11
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+ zTIL01
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+ zTIL25
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+ zTIL18
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+ zhuehu
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+ zdiplg
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+ zdiplm
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+ znicar
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+ zluxur
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+ tdacts
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+ tdactn
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+ tzopol
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+ vcuspi
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+ rrottb
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+ rtuber
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+ hcompr
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+ aburma
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+ sspont
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+ sbicol
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+ ppanic
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+ irugos
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+ ttrian
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+ hconto
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+ blagur
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+ crefra
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+ ccitra
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+ sscopa
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+ smicro
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+ avirgi
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+ agerar
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+ achine
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+ snutan
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+ udigit
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+ etrips
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+ telega
species_metadata.tsv ADDED
@@ -0,0 +1,37 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ Tip Species Prefix
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+ zB73v5 Zea mays var. B73 Zm-B73-REFERENCE-NAM-5.0.fa
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+ zTIL11 Zea mays ssp. parviglumis TIL11 Zv-TIL11-REFERENCE-PanAnd-1.0
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+ zTIL01 Zea mays ssp. Parviglumis TIL01 Zv-TIL01-REFERENCE-PanAnd-1.0
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+ zTIL25 Zea mays ssp. mexicana TIL25 Zx-TIL25-REFERENCE-PanAnd-1.0
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+ zTIL18 Zea mays ssp. mexicana TIL18 Zx-TIL18-REFERENCE-PanAnd-1.0
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+ zhuehu Zea-mays-ssp-huehuetena Zh-RIMHU001-REFERENCE-PanAnd-1.0
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+ zdiplg Zea diploperennis (gigi) Zd-Gigi-REFERENCE-PanAnd-1.0
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+ zdiplm Zea diploperennis momo Zd-Momo-REFERENCE-PanAnd-1.0
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+ znicar Zea nicaraguensis Zn-PI615697-REFERENCE-PanAnd-1.0
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+ zluxur Zea luxurians Zl-RIL003-REFERENCE-PanAnd-1.0
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+ tdacts Tripsacum dactyloides-FL Td-FL_9056069_6-REFERENCE-PanAnd-1.0
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+ tdactn Tripsacum dactyloides-KS Td-KS_B6_1-REFERENCE-PanAnd-1.0
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+ tzopol Tripsacum zopolitense Tz-DC_05_58_3A-DRAFT-PanAnd-1.0
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+ vcuspi Vossia cuspidata Vc-Pasquet1098-DRAFT-PanAnd-1.0
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+ rrottb Rhytacne rottboelloides Rr-Malcomber3106-DRAFT-PanAnd-1.0
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+ rtuber Rottboellia tuberculosa Rt-Layton_Zhong169-DRAFT-PanAnd-1.0
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+ hcompr Hermarthria compressa Hp-KelloggPI404118-DRAFT-PanAnd-1.0
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+ aburma Andropogon burmanicus Ab-Traiperm_572-DRAFT-PanAnd-1.0
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+ sspont Saccharum spontaneum
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+ sbicol Sorghum bicolor Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel
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+ ppanic Pogonatherum paniceum Pi-Clark-DRAFT-PanAnd-1.0
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+ irugos Isachaemum rugosum Ir-Pasquet1136-DRAFT-PanAnd-1.0
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+ ttrian Themeda triandra Tt-AUB21_1-DRAFT-PanAnd-1.0
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+ hconto Heteropogon contortus Hc-AUB53_1-DRAFT-PanAnd-1.0
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+ blagur Bothriochloa laguroides Bl-K1279B-DRAFT-PanAnd-1.0
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+ crefra Cymbopogon refractus Cr-AUB069-DRAFT-PanAnd-1.0
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+ ccitra Cymbopogon citratus Cc-PI314907-DRAFT-PanAnd-1.0
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+ sscopa Schizachyrium scoparium Ss-CAM1384-DRAFT-PanAnd-1.0
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+ smicro Schizachyrium microstachyum Sm-PI203595-DRAFT-PanAnd-1.0
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+ avirgi Andropogon virginicus Av-Kellogg1287_8-REFERENCE-PanAnd-1.0
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+ agerar Andropogon geradii Ag-CAM1351-DRAFT-PanAnd-1.0
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+ achine Andropogon chinensis Ac-Pasquet1232-DRAFT-PanAnd-1.0
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+ snutan Sorghastrum nutans Sn-CAM1369-DRAFT-PanAnd-1.0
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+ udigit Urelytrum digitatum Ud-Pasquet1171-DRAFT-PanAnd-1.0
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+ etrips Elionorus tripsacoides Et-Layton_Zhong168-DRAFT-PanAnd-1.0
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+ telega Thelopogon elegans Te-Pasquet1246-DRAFT-PanAnd-1.0
tree.nh ADDED
@@ -0,0 +1 @@
 
 
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+ (((((((((((zB73v5:0.08453,(zTIL11:0.06000,zTIL01:0.06190)Anc34:0.01000)Anc30:0.01000,(zTIL25:0.03386,zTIL18:0.04439)Anc31:0.01511)Anc26:0.01510)Anc23:0.13391,zhuehu:0.10000)Anc18:0.10000,(zdiplg:0.10000,zdiplm:0.10000)Anc19:0.10000)Anc13:0.10000,(znicar:0.10000,zluxur:0.10000)Anc14:0.10000)Anc10:0.10000,((tdacts:0.02908,tdactn:0.02587)Anc15:0.09665,tzopol:0.17250)Anc11:0.05199)Anc06:0.06710,(vcuspi:0.06710,rrottb:0.07586)Anc07:0.00244)Anc04:0.00135,((rtuber:0.06137,hcompr:0.07372)Anc08:0.00570,(aburma:0.07928,(((sspont:0.05872,sbicol:0.05974)Anc20:0.00244,(ppanic:0.07080,irugos:0.07087)Anc21:0.00213)Anc16:0.00118,(((((ttrian:0.05650,hconto:0.05838)Anc32:0.00767,blagur:0.06360)Anc27:0.00311,(crefra:0.02652,ccitra:0.02649)Anc28:0.03930)Anc24:0.00138,((((sscopa:0.01935,smicro:0.02805)Anc35:0.01563,avirgi:0.03516)Anc33:0.01000,agerar:0.04566)Anc29:0.00310,achine:0.04968)Anc25:0.01667)Anc22:0.00324,snutan:0.07105)Anc17:0.00120)Anc12:0.00115)Anc09:0.00412)Anc05:0.00047)Anc03:0.00230,(udigit:0.07484,etrips:0.08384)Anc02:0.00494)Anc01:0.04101,telega:0.04101)Anc00:0.00000;