15 research outputs found
Alcaide_etal_PeerJ_MHC_classI_alignment
This alignment was used in the analysis of the paper in PeerJ by M. Alcaide, M. Liu and S. Edwards entitled "Major Histocompatibility Complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3". The alignment begins on the first position of the codon and was made according to methods described in the paper. Taxa without Genbank numbers are original data; Genbank nubmers for these sequences can be found on Genbank. Taxa with Genbank numbers were taken from Genbank
Cy_Gsnap-alignment
Sam files of the 38 individuals with two types of alignment to a Pseudo-Reference-Genome (PRG), to the American Crow (Cy_AmericanCrow) and the Zebra Finch (Cy_ZebraFinch), performed with Gsnap and after all filters (clone filter, optical duplicates and mapping quality)
Cy_STACKS_output
STACKS output from the correction module (rx_stacks) of ref_map (two PRG: PRG_AmericanCrow and PRG_ZebraFinch) and de_novo (run 1 and run 2 separate: Denovo_R1 and Denovo_R2) pipelines and populations maps used (Cy_2POP.txt and Cy_3POP.txt). Included are the catalog.tags, de-novo assemblies and output of the populations module. Each directory includes summary statistics per locus and overall, and all SNP data in STRUCTURE, FASTA, Genpop, PLINK and VCF format
Cy_Baypass_input
Input used in BayPass analyses including genetic (Cy.BayPass2allele.count.txt) and environmental (Cy.BayPass-var-X.txt) data. The environmental data are in separate files for each of the final nine climatic variables used (e.g Cy.BayPass-var-bio4.txt). The order of the samples are in file "ORDER-SAMPLES-BayPass.txt"
Cy_FASTQ
FASTq sequences of 38 individuals used, with their corresponding barcode from the sequencing. See file "Cy_GENERAL-DATA-ID-GEO-CATALOG.txt" to know the general information of the samples
Cy_GENERAL-DATA-ID-GEO-CATALOG
General information of the 38 samples: catalog-voucher from the National Ornithology Collection (UNAM, Mexico), sample ID (barcodes from the sequencing) geographic position (longitude and latitude), the corresponding operative-geogaraphic-unit (OGU), vegetation type and number of the sampling point (see Figure 1 in the article)
Cy_Fasta_BLAST
FASTA file of consensus sequences containing all SNPs (CLOCUS_) used in the study and BLAST (MATCHCLOCUS and Q_Query=) results of these loci
yuhina_relatedness_for_dryad_051815
This is relatedness matrix in yuhina breeding group
yuhina_extra_pair_offspring_for_dryad_051815
Data of extra paired offsprings id and their assigned biological parents
Cy_LFMM_input
Input used in LFMM analyses including genetic (Cy.lfmm) and environmental (Cy.lfmm.env) data for each individual. The order of the samples are in file "ORDER-SAMPLES-plink-LFMM.txt