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Data for Publications


Phylogenetic data of Domesticated Region I and Domesticated Region II:
Original data for manuscript “Selective sweep with significant positive selection serves as the driving force for the differentiation of japonica and indica rice cultivars”

Region I (for Figure 1)

Region II (for Figure 2)

Phylogenetic trees were saved in PHYLIP format


Tetrads Genotypes:
In each file, the first column is marker positions in the genome. The second and third columns are parental genotypes, the fourth to seventh columns are genotypes of the four spore in this tetrad. In Arabidopsis, the tetrad seeds are diploid, the genotype of meiotic seed is represented by 'C' or 'H', 'C' indicates homogenous Col genotype, ‘H’ indicates heterozygous Col/Ler genotype.

A.zip

C1.zip

C2.zip

C3.zip

N1.zip

N2.zip

N3.zip

N4.zip

S1.zip

S2.zip


Bumblebee Genotypes:
The genotypes of 32 drones at all marker sites are recorded in the two files: “Colony.I.genotype” and “Colony.II.genotype”.

In each file, the first column is marker positions in the genome. From the second column to the last column, each column represents a sample, sample name is the first item in this column.

Colony I genotype

Colony II genotype


Pseudogenes:

List of Candidate Pseudogenes

ReadMe

Wang L, Si W, Yao Y, Tian D, Araki H. Yang S. (2012) Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. Plos One 7(12): e51769


Primate:

Human-OtherPrimate-Mouse:

Homo-Callithirx-Mus.align.cds.zip

Homo-Callithirx-Mus.align.pep.zip

Homo-Gorilla-Mus.align.cds.pep.zip

Homo-Gorilla-Mus.align.pep.zip

Homo-Macaca-Mus.align.cds.zip

Homo-Macaca-Mus.align.pep.zip

Homo-Nomascus-Mus.align.cds.zip

Homo-Nomascus-Mus.align.pep.zip

Homo-Otolemur-Mus.align.cds.zip

Homo-Otolemur-Mus.align.pep.zip

Homo-Pan-Mus.align.cds.zip

Homo-Pan-Mus.align.pep.zip

Homo-Pongo-Mus.align.cds.zip

Homo-Pongo-Mus.align.pep.zip

HumanSNP:

homo-homo.snp-pan.aln.cds.zip

homo-homo.snp-pan.aln.pep.zip

human.cds.SNP.zip

Human.mutation.codon.zip

TripletOfPrimates:

callithrix-otolemur-mus.aln.cds.zip

callithrix-otolemur-mus.aln.pep.zip

homo-pan-gorilla.aln.cds.zip

homo-pan-gorilla.aln.pep.zip

gorilla-pongo-nomascus.aln.cds.zip

gorilla-pongo-nomascus.aln.pep.zip

nomascus-macaca-callithrix.aln.cds.zip

nomascus-macaca-callithrix.aln.pep.zip



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