Data for "Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns"
Creators: name: Joao Machado
name: Siby Philip
name: Maldonado, Emanuel
name: Johnson, Warren E.
name: O’Brien, Stephen J.
name: Antunes, Agostinho
Publisher: name: figshare
Year: 2016
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: The data contained in them pretains to the manuscript"Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns"<br>2 zip files:<br><b> 1) GENES.zip </b>- This file contains 236 folders with the genes used for evolutionary analysis:<br> ACHE/ ACLY/ ACVR1B/ ACVR2B/ ADAMTS2/ ADM/ AGPAT2/ ALKBH1/ ALPL/ AMBN/ AMTN/ ANKH/ ANKRD11/ ANTXR1/ APC/ AQP1/ AQP3/ AQP5/ AQP6/ ASPN/ ATR/ AXIN2/ BARX1/ BAX/ BAZ1B/ BCL11B/ BCL2L11/ BCOR/ BGLAP/ BMP2/ BMP4/ BMP7/ BMPR1A/ BRAF/ BSG/ CA2/ CBX2/ CCL2/ CCND1/ CD34/ CD86/ CDKN1A/ CDKN1B/ CDO1/ CDON/ CHUK/ CLCN5/ CLCN7/ COL10A1/ COL1A1/ COL1A2/ COL7A1/ CSF1/ CSF1R/ CSF2/ CSF3R/ CTNNA1/ CTNNB1/ CTSK/ DCN/ DIAP1/ DICER1/ DISP1/ DLL1/ DLX1/ DLX2/ DLX5/ DMP1/ DMRT3/ DSPP/ EDA/ EDAR/ EDARADD/ EDN1/ EDNRA/ ENAM/ ERBB2/ ERBB3/ ERBB4/ EVC/ FAM20A/ FAM20C/ FGF10/ FGF4/ FGF8/ FGFR1/ FGFR2/ FGFR3/ FMOD/ FOS/ FOXA2/ FST/ FUZ/ GALC/ GATA6/ GJA/ GLI2/ GLI3/ GTF2IRD1/ HAND1/ HAND2/ HDAC1/ HDAC2/ HOXB1/ HOXB8/ HRAS1/ ID3/ IDUA/ IFT88/ IL1R1/ INHBA/ INHBB/ IRF6/ ITGA11/ ITGA6/ JAG1/ JAG2/ KLK4/ LAMA3/ LAMA5/ LAMB1/ LEF1/ LHX8/ LMNA/ LPAR1/ LRP4/ LRP6/ LTBP1/ LTBP3/ MAP3K11/ MECOM/ MECP2/ MITF/ MMP14/ MMP20/ MSX1/ MSX2/ MTF2/ MYO5A/ NF2/ NFATC1/ NFE2L2/ NFIC/ NFKB1/ NFKB2/ NGFR/ NKX2-3/ NOS2/ NOTCH2/ NPHP3/ NPR2/ NR3C1/ ODAM/ OSR1/ OSR2/ OSTM1/ PAM/ PAPSS2/ PAX3/ PAX6/ PAX9/ PDGFRA/ PITX2/ PKD1/ PORCN/ POSTN/ POU1F1/ PPARA/ PRKCB/ PRRX2/ PRXX1/ PTCH1/ PTHLH/ PTPN9/ PVR1L/ PVRL3/ RAI1/ RBL1/ RBL2/ RSPO2/ RUNX2/ S100B/ SATB2/ SCN10A/ SCN5A/ SDC1/ SFPI1/ SH3PXD2B/ SHH/ SIM2/ SIRT6/ SLC39A13/ SLC4A2/ SLC4A4/ SLX4/ SMN1/ SMO/ SOSTDC1/ SOX3/ SP3/ SP6/ SPRY2/ SPRY4/ SRC/ STAG1/ SULF1/ SULF2/ TBX1/ TCF7L2/ TCFAP2A/ TCIRG1/ TFE3/ TGFB1/ TGFB2/ TGFB3/ TNC/ TNFRSF11A/ TNFRSF11B/ TNFRSF19/ TNFSF11/ TRAF6/ TRP53/ TRP63/ TUFT1/ UROS/ VAX1/ VEGFA/ WHSC1/ WLS/ WNT10A/ WNT6/ WNT7B/ ZIC3/ ZIC5/ ZMPSTE24/ ZNF22/<br> Each folder contains 5 sub-folders:<br> FASTA/ - Gene alingment GBLOCKS/ - 2 files: Gene full sequence (*.fas) Gene trimmed gene (*.fas-gb) MRAIC_GENE_TREE/ - Result tree from MrAIC applying the best evolutionary model obtained using BIC using the followin annotation: "GENE NAME".BIC-"BEST MODEL".tre GENE_TREE/ - Results of CODEML M0_7_8/ - Results of Model 0, 7 and 8 in a single file, M1_2/ - Results of Model 1 and 2 in a single file, M8a/ - Results of Model 8a SPECIES_TREE/ - Results of CODEML M0_7_8/ - Results of Model 0, 7 and 8 in a single file, M1_2/ - Results of Model 1 and 2 in a single file, M8a/ - Results of Model 8a<br> <b> 2) PARAMETERS.zip</b> - This file contains the used species tree, and 3 codeml parameter templates: Species_tree.nwk - Mammalian species tree used in CODEML codeml_M0_7_8.ctl - parameters file template for Models 0, 7 and 8a codeml_M1_2.ctl - parameters file template for Models 1 and 2 codeml_M8a.ctl - parameters file template for Model 8a