Index of /download/genome_alignments

Icon  Name                          Last modified      Size  Description
[PARENTDIR] Parent Directory                                   -   
[DIR] C_albicans_SC5314/            2017-12-19 13:11    -   
[DIR] C_dubliniensis_CD36/          2017-12-19 13:16    -   
[DIR] C_glabrata_CBS138/            2017-12-19 13:19    -   
[DIR] C_parapsilosis_CDC317/        2017-12-19 13:23    -   
[   ] albicans_group.maf.gz         2017-12-19 09:32   12M  
[   ] albicans_group_B.maf.gz       2017-12-19 09:33   12M  
[   ] albicans_group_tree.par       2017-12-19 09:50   44   
[   ] candida_lodderomyces.maf.gz   2017-12-19 09:34   27M  
[   ] candida_lodderomyces_B.maf.gz 2017-12-19 09:35   27M  
[   ] candida_lodderomyces_tree.par 2017-12-19 09:51   96   
[   ] ctg_clade.maf.gz              2017-12-19 09:37   44M  
[   ] ctg_clade_B.maf.gz            2017-12-19 09:38   44M  
[   ] ctg_clade_tree.par            2017-12-19 09:51  142   
[   ] glabrata_group.maf.gz         2017-12-19 09:42   11M  
[   ] glabrata_group_tree.par       2017-12-19 09:54   43   
[   ] nakaseomyces_candida.maf.gz   2017-12-19 09:43   19M  
[   ] nakaseomyces_candida_tree.par 2017-12-19 09:54   75   
[   ] parapsilosis_group.maf.gz     2017-12-19 09:44   12M  
[   ] parapsilosis_group_tree.par   2017-12-19 09:56   51   
[   ] saccharomycetales.maf.gz      2017-12-19 09:40   62M  
[   ] saccharomycetales_B.maf.gz    2017-12-19 09:41   62M  
[   ] saccharomycetales_tree.par    2017-12-19 09:52  179   
[   ] wgd_clade.maf.gz              2017-12-19 11:51   39M  
[   ] wgd_clade_tree.par            2017-12-19 09:55  128   

The /download/genome_alignments/ directory and subdirectories contain 
whole-genome multiple sequence alignments, phylogenetic trees, and 
conservation scores for Candida-related species.

NOTE: Separate alignments were produced for the two haplotypes 
[A and B] of C. albicans SC5314 Assembly 22. Filenames for alignments
for the B haplotype contain a "_B" tag.

This (top-level) directory contains the unprocessed alignments and 
guide trees. Alignments were produced with the MULTIZ/TBA package 
(Blanchette et al, Genome Res. 2004 14(4):708; PMID 15060014) 
from the Miller lab: http://www.bx.psu.edu/miller_lab/
The sources for the genomic DNA sequences used are listed below. All-by-all 
pairwise alignments were produced using the all_bz program, from which 
multiple alignments were made using the tba program. Default parameters 
were used for both programs. The resulting alignments are in MAF format, 
described here: https://genome.ucsc.edu/FAQ/FAQformat.html#format5

Guide trees are rooted and have no branch lengths. Phylogenies are based
on Fitzpatrick et al. (BMC Evolutionary Biology 2006, 6:99; PMID 17121679),
Wang et al. (BMC Evolutionary Biology 2009, 9:195; PMID 19664262), and
Gabaldon et al. (BMC Genomics 2013, 14:623; PMID 24034898). Trees are in 
Newick format, described here: 
http://evolution.genetics.washington.edu/phylip/newicktree.html

The four species-specific subdirectories contain alignments projected 
with that species as the "reference". The subdirectories also contain 
conservation scores based on those reference species alignments:
C_albicans_SC5314/
C_dubliniensis_CD36/
C_glabrata_CBS138/
C_parapsilosis_CDC317/

The files in the present directory are:

albicans_group.maf.gz
	Alignment of the genomes of 3 closely-related species: C. albicans SC5314, 
	C. dubliniensis CD36, and C. tropicalis MYA-3404
albicans_group_B.maf.gz
	As albicans_group.maf.gz, but using the B haplotype of C. albicans SC5314
albicans_group_tree.par
	Guide tree for albicans_group.maf.gz
candida_lodderomyces.maf.gz
	Alignment of the genomes of 6 related species: C. albicans SC5314, 
	C. dubliniensis CD36, C. tropicalis MYA-3404, C. parapsilosis CDC317,
	C. orthopsilosis Co 90-125, and L. elongisporus NRLL YB-4239
candida_lodderomyces_B.maf.gz
	As candida_lodderomyces.maf.gz, but using the B haplotype of C. albicans SC5314
candida_lodderomyces_tree.par
	Guide tree for candida_lodderomyces.maf.gz
ctg_clade.maf.gz
	Alignment of the genomes of 9 species in the "CTG clade": C. albicans SC5314, 
	C. dubliniensis CD36, C. tropicalis MYA-3404, C. parapsilosis CDC317,
	C. orthopsilosis Co 90-125, L. elongisporus NRLL YB-4239, C. guilliermondii ATCC 6260,
	D. hansenii CBS767, and C. lusitaniae ATCC 42720
ctg_clade_B.maf.gz
	As ctg_clade.maf.gz, but using the B haplotype of C. albicans SC5314
ctg_clade_tree.par
	Guide tree for ctg_clade.maf.gz
glabrata_group.maf.gz
	Alignment of the genomes of 3 closely-related species: C. glabrata CBS138, 
	C. bracarensis CBS 10154, and C. nivariensis CBS 9983
glabrata_group_tree.par
	Guide tree for glabrata_group.maf.gz
nakaseomyces_candida.maf.gz
	Alignment of the genomes of 5 related species: C. glabrata CBS138, 
	C. bracarensis CBS 10154, C. nivariensis CBS 9983, N. bacillisporus CBS 7720,
	and C. castellii CBS 4332
nakaseomyces_candida_tree.par
	Guide tree for nakaseomyces_candida.maf.gz
parapsilosis_group.maf.gz
	Alignment of the genomes of 3 closely-related species: C. parapsilosis CDC317,
	C. orthopsilosis Co 90-125, and L. elongisporus NRLL YB-4239
parapsilosis_group_tree.par
	Guide tree for parapsilosis_group.maf.gz
saccharomycetales.maf.gz
	Alignment of the genomes of 12 budding yeast species: C. albicans SC5314, 
	C. dubliniensis CD36, C. parapsilosis CDC317, L. elongisporus NRLL YB-4239, 
	D. hansenii CBS767, C. glabrata CBS138, C. bracarensis CBS 10154,  
	N. bacillisporus CBS 7720, S. cerevisiae S288C, S. castellii NRRL-Y12630,
	A. gossypii ASM9102, and Y. lipolytica CLIB122
saccharomycetales_B.maf.gz
	As saccharomycetales.maf.gz, but using the B haplotype of C. albicans SC5314
saccharomycetales_tree.par
	Guide tree for saccharomycetales.maf.gz
wgd_clade.maf.gz
	Alignment of the genomes of 9 species in the "whole-genome duplication clade":
	C. glabrata CBS138, C. bracarensis CBS 10154, C. nivariensis CBS 9983, 
	N. bacillisporus CBS 7720, C. castellii CBS 4332, S. cerevisiae S288C,
	S. mikatae IFO1815, S. bayanus 623-6C, and S. castellii NRRL-Y12630
wgd_clade_tree.par
	Guide tree for wgd_clade.maf.gz

Sequence Sources
	Genome sequences were downloaded in November 2017 from the following sources:
	CGD (http://www.candidagenome.org/download/sequence/)
		C. albicans SC5314 Assembly 22, haplotypes A and B
		C. dubliniensis CD36
		C. tropicalis MYA-3404
		C. parapsilosis CDC317
		C. orthopsilosis Co 90-125
		L. elongisporus NRLL YB-4239
		C. guilliermondii ATCC 6260
		D. hansenii CBS767
		C. lusitaniae ATCC 42720
		C. glabrata CBS138
	SGD
		S. cerevisiae S288C (https://downloads.yeastgenome.org/sequence/S288C_reference/)
		Other Saccharomyces species (https://downloads.yeastgenome.org/sequence/fungi/)
			S. mikatae IFO1815
			S. bayanus 623-6C
			S. castellii NRRL-Y12630
	NCBI Genome
		C. bracarensis CBS 10154 (https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAPU01)
		C. nivariensis CBS 9983 (https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAPV01)
		N. bacillisporus CBS 7720 
			(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/046/975/GCA_001046975.1_ASM104697v1)
		C. castellii CBS 4332 (https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=CAPW01)
		Yarrowia lipolytica CLIB122
			(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/525/GCA_000002525.1_ASM252v1)
	Ensembl Fungi
		A. gossypii ASM9102v1
			(ftp://ftp.ensemblgenomes.org/pub/fungi/release-37/fasta/ashbya_gossypii/dna/)

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Alignment files are gzip compressed. There are several freely available
software options for decompressing gzipped files using Windows.  The
software and other useful information is available on these web sites:
- WinZip (http://www.winzip.com/)
- Stuffit (http://www.stuffit.com/)
- Gzip (http://www.gzip.org/
   
and the gzip user's manual:
http://www.math.utah.edu/docs/info/gzip_toc.html

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