1.   Ensembl v64 Human-Chimpanzee 
2.   Ensembl v64 Human-Macaque 
3.   Gencode v10 Human-Chimpanzee 
4.   Gencode v10 Human-Cacaque 
5.   Gencode v10 Human-Chimpanzee-Macaque 

1. Ensembl v64 Human-Chimpanzee 

This directory contains human-chimpanzee orthologs identified by XSAnno, based on Ensembl v64 human annotation

Transcript exons:
  - Ensembl.v64.fullTransExon.hg19TopanTro2.hg19.bed: Coordinates of human-chimpanzee orthologous exons on human reference genome hg19
  - Ensembl.v64.fullTransExon.hg19TopanTro2.panTro2.bed: Coordinates of human-chimpanzee orthologous exons on chimpanzee reference genome panTro2

Composite gene models - exons from the same gene whose genomic locations overlap are merged
  - Ensembl.v64.compGene.hg19TopanTro2.hg19.interval: Coordinates of human-chimpanzee orthologous genes on human reference genome hg19
  - Ensembl.v64.compGene.hg19TopanTro2.panTro2.interval: Coordinates of human-chimpanzee orthologous genes on chimpanzee reference genome panTro2


  
2.   Ensembl v64 Human-Macaque 
  
This directory contains human-macaque orthologs identified by XSAnno, based on Ensembl v64 human annotation

Transcript exons:
  - Ensembl.v64.fullTransExon.hg19TorheMac2.hg19.bed: Coordinates of human-macaque orthologous exons on human reference genome hg19
  - Ensembl.v64.fullTransExon.hg19TorheMac2.rheMac2.bed: Coordinates of human-macaque orthologous exons on macaque reference genome rheMac2

Composite gene models - exons from the same gene whose genomic locations overlap are merged
  - Ensembl.v64.compGene.hg19TorheMac2.hg19.interval: Coordinates of human-macaque orthologous genes on human reference genome hg19
  - Ensembl.v64.compGene.hg19TorheMac2.rheMac2.interval: Coordinates of human-macaque orthologous genes on macaque reference genome rheMac2

  
3.   Gencode v10 Human-Chimpanzee

This directory contains human-chimpanzee orthologs identified by XSAnno, based on Gencode v10 human annotation

Transcript exons - exons are uniqued based on locations:
  - Gencode.v10.fullTransExon.hg19TopanTro2.hg19.bed: Coordinates of human-chimpanzee orthologous exons on human reference genome hg19
  - Gencode.v10.fullTransExon.hg19TopanTro2.panTro2.bed: Coordinates of human-chimpanzee orthologous exons on chimpanzee reference genome panTro2

 
4.   Gencode v10 Human-Macaque 

This directory contains human-macaque orthologs identified by XSAnno, based on Gencode v10 human annotation

Transcript exons - exons are uniqued based on locations:
  - Gencode.v10.fullTransExon.hg19TorheMac2.hg19.bed: Coordinates of human-macaque orthologous exons on human reference genome hg19
  - Gencode.v10.fullTransExon.hg19TorheMac2.rheMac2.bed: Coordinates of human-macaque orthologous exons on macaque reference genome rheMac2
 
  
5.   Gencode v10 Human-Chimpanzee-Macaque 

This directory contains human-chimpanzee-macaque 1:1:1 orthologs identified by XSAnno, based on Gencode v10 human annotation

Transcript exons - exons are uniqued based on locations:
  - Gencode.v10.HPR.transExon.hg19.interval: Coordinates of human-chimpanzee-macaque orthologous exons on human reference genome hg19
  - Gencode.v10.HPR.transExon.panTro3.interval: Coordinates of human-chimpanzee-macaque orthologous exons on chimpanzee reference genome panTro2
  - Gencode.v10.HPR.transExon.rheMac2.interval: Coordinates of human-chimpanzee-macaque orthologous exons on macaque reference genome rheMac2
 
Composite gene models - exons from the same gene whose genomic locations overlap are merged
  - Gencode.v10.HPR.compGene.hg19.interval: Coordinates of human-chimpanzee-macaque orthologous genes on human reference genome hg19
  - Gencode.v10.HPR.compGene.panTro3.interval: Coordinates of human-chimpanzee-macaque orthologous genes on chimpanzee reference genome panTro2
  - Gencode.v10.HPR.compGene.rheMac2.interval: Coordinates of human-chimpanzee-macaque orthologous genes on macaque reference genome rheMac2