Index of /download/genome_alignments/C_albicans_SC5314

Icon  Name                                                          Last modified      Size  Description
[DIR] Parent Directory - [   ] C_albicans_SC5314_albicans_group.noncons.mod 19-Dec-2017 11:55 414 [   ] C_albicans_SC5314_albicans_group.tar.gz 19-Dec-2017 10:07 11M [   ] C_albicans_SC5314_albicans_group_B.tar.gz 19-Dec-2017 10:14 11M [   ] C_albicans_SC5314_albicans_group_phyloP_scores.wig.gz 19-Dec-2017 12:08 6.8M [   ] C_albicans_SC5314_albicans_group_phyloP_scores_B.wig.gz 19-Dec-2017 12:09 6.5M [   ] C_albicans_SC5314_candida_lodderomyces.noncons.mod 19-Dec-2017 13:09 519 [   ] C_albicans_SC5314_candida_lodderomyces.tar.gz 19-Dec-2017 10:21 20M [   ] C_albicans_SC5314_candida_lodderomyces_B.tar.gz 19-Dec-2017 10:26 20M [   ] C_albicans_SC5314_candida_lodderomyces_phyloP_scores.wig.gz 19-Dec-2017 12:10 10M [   ] C_albicans_SC5314_candida_lodderomyces_phyloP_scores_B.wig.gz 19-Dec-2017 12:10 10M [   ] C_albicans_SC5314_ctg_clade.noncons.mod 19-Dec-2017 13:10 621 [   ] C_albicans_SC5314_ctg_clade.tar.gz 19-Dec-2017 10:32 28M [   ] C_albicans_SC5314_ctg_clade_B.tar.gz 19-Dec-2017 10:34 28M [   ] C_albicans_SC5314_ctg_clade_phyloP_scores.wig.gz 19-Dec-2017 12:11 13M [   ] C_albicans_SC5314_ctg_clade_phyloP_scores_B.wig.gz 19-Dec-2017 12:12 13M [   ] C_albicans_SC5314_saccharomycetales.noncons.mod 19-Dec-2017 13:11 714 [   ] C_albicans_SC5314_saccharomycetales.tar.gz 19-Dec-2017 10:42 29M [   ] C_albicans_SC5314_saccharomycetales_B.tar.gz 19-Dec-2017 10:44 29M [   ] C_albicans_SC5314_saccharomycetales_phyloP_scores.wig.gz 19-Dec-2017 12:13 12M [   ] C_albicans_SC5314_saccharomycetales_phyloP_scores_B.wig.gz 19-Dec-2017 12:14 12M
The /download/genome_alignments/C_albicans_SC5314/ directory contains 
whole-genome multiple sequence alignments, conservation scores, and 
phylogenetic models for Candida albicans SC5314.

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.

Alignments in this directory were produced from the unprocessed alignments
in the parent directory (/download/genome_alignments/) using utility programs in
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/. They were first projected
with C. albicans SC5314 as reference species using the program "maf_project",
then ordered by species and location using the program "maf_order", and finally split
into separate chromosome-specific files using the program "mafFind". They are provided 
here as archived and compressed directories, which were produced using the Linux 
utilities 'tar' and 'gzip'. Alignment files within the directories are in MAF format, 
described here: https://genome.ucsc.edu/FAQ/FAQformat.html#format5

Initial phylogenetic models were produced using the program phyloFit from
the PHAST package (Siepel et al, Genome Res. 2005 15(8):1034; PMID 16024819), 
available here: http://compgen.cshl.edu/phast/. Input for the program were
the reference-species alignments in this directory and the guide trees in the
parent directory (/download/genome_alignments/). Models were subsequently optimized
and refined using the program phastCons from the PHAST package, as described in
the above paper and here: http://compgen.cshl.edu/phast/phastCons-HOWTO.html.
For optimization, the target Phylogenetic Information Threshole (PIT) was 8.0
for each model. The optimized non-conserved model for each alignment is provided
in this directory, and the final parameters used to produce them are listed below.

Conservation scores were produced using the phyloP program in the PHAST package.
The likelihood ratio test (LRT) method was used. Input for the program were the
alignments and optimized non-conserved models in this directory. The scores are in 
"wig" format, described here: https://genome.ucsc.edu/goldenpath/help/wiggle.html.

The files in the present directory are:

C_albicans_SC5314_albicans_group.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_albicans_SC5314_albicans_group.tar.gz (same model for both haplotypes).
        The parameters used were: target coverage (gamma) = 0.43, expected element length
        (omega) = 12.
C_albicans_SC5314_albicans_group.tar.gz
	Archived and compressed directory containing alignments of the genomes of 3 
	closely-related species: C. albicans SC5314, C. dubliniensis CD36, and 
	C. tropicalis MYA-3404. The alignments are projected using C. albicans SC5314 
	as reference species, and separated into chromosome-specific files.
C_albicans_SC5314_albicans_group_B.tar.gz
	As C_albicans_SC5314_albicans_group.tar.gz, but using the B haplotype of 
	C. albicans SC5314.
C_albicans_SC5314_albicans_group_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_albicans_SC5314_albicans_group.tar.gz
C_albicans_SC5314_albicans_group_phyloP_scores_B.wig.gz
	As C_albicans_SC5314_albicans_group_phyloP_scores.wig.gz, but using the B haplotype 
	of C. albicans SC5314.
C_albicans_SC5314_candida_lodderomyces.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_albicans_SC5314_candida_lodderomyces.tar.gz. (same model for both haplotypes).
        The parameters used were: target coverage (gamma) = 0.39, expected element length
        (omega) = 12.
C_albicans_SC5314_candida_lodderomyces.tar.gz
	Archived and compressed directory containing alignments 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. 
	The alignments are projected using C. albicans SC5314 as reference species, and
	separated into chromosome-specific files.
C_albicans_SC5314_candida_lodderomyces_B.tar.gz
	As C_albicans_SC5314_candida_lodderomyces.tar.gz, but using the B haplotype of 
	C. albicans SC5314.
C_albicans_SC5314_candida_lodderomyces_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_albicans_SC5314_candida_lodderomyces.tar.gz
C_albicans_SC5314_candida_lodderomyces_phyloP_scores_B.wig.gz
	As C_albicans_SC5314_candida_lodderomyces_phyloP_scores.wig.gz, but using the B 
	haplotype of C. albicans SC5314.
C_albicans_SC5314_ctg_clade.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_albicans_SC5314_ctg_clade.tar.gz. (same model for both haplotypes). The parameters
        used were: target coverage (gamma) = 0.37, expected element length (omega) = 12.
C_albicans_SC5314_ctg_clade.tar.gz
	Archived and compressed directory containing alignments 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. 
	The alignments are projected using C. albicans SC5314 as reference species, and
	separated into chromosome-specific files.
C_albicans_SC5314_ctg_clade_B.tar.gz
	As C_albicans_SC5314_ctg_clade.tar.gz, but using the B haplotype of 
	C. albicans SC5314.
C_albicans_SC5314_ctg_clade_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_albicans_SC5314_ctg_clade.tar.gz
C_albicans_SC5314_ctg_clade_phyloP_scores_B.wig.gz
	As C_albicans_SC5314_ctg_clade_phyloP_scores.wig.gz, but using the B haplotype 
	of C. albicans SC5314.
C_albicans_SC5314_saccharomycetales.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_albicans_SC5314_saccharomycetales.tar.gz. (same model for both haplotypes).
        The parameters used were: target coverage (gamma) = 0.36, expected element length
        (omega) = 12.
C_albicans_SC5314_saccharomycetales.tar.gz
	Archived and compressed directory containing alignments 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. 
	The alignments are projected using C. albicans SC5314 as reference species, and
	separated into chromosome-specific files.
C_albicans_SC5314_saccharomycetales_B.tar.gz
	As C_albicans_SC5314_saccharomycetales.tar.gz, but using the B haplotype of 
	C. albicans SC5314.
C_albicans_SC5314_saccharomycetales_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_albicans_SC5314_saccharomycetales.tar.gz
C_albicans_SC5314_saccharomycetales_phyloP_scores_B.wig.gz
	As C_albicans_SC5314_saccharomycetales_phyloP_scores.wig.gz, but using the B 
	haplotype of C. albicans SC5314.


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Alignment and conservation score 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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