Index of /download/genome_alignments/C_parapsilosis_CDC317

Icon  Name                                                            Last modified      Size  Description
[PARENTDIR] Parent Directory                                                                     -   
[SND] C_parapsilosis_CDC317_candida_lodderomyces.noncons.mod          2017-12-19 13:22  520   
[   ] C_parapsilosis_CDC317_candida_lodderomyces.tar.gz               2017-12-19 11:16   18M  
[   ] C_parapsilosis_CDC317_candida_lodderomyces_phyloP_scores.wig.gz 2017-12-19 12:29  9.6M  
[SND] C_parapsilosis_CDC317_ctg_clade.noncons.mod                     2017-12-19 13:22  622   
[   ] C_parapsilosis_CDC317_ctg_clade.tar.gz                          2017-12-19 11:21   27M  
[   ] C_parapsilosis_CDC317_ctg_clade_phyloP_scores.wig.gz            2017-12-19 12:30   12M  
[SND] C_parapsilosis_CDC317_parapsilosis_group.noncons.mod            2017-12-19 13:20  421   
[   ] C_parapsilosis_CDC317_parapsilosis_group.tar.gz                 2017-12-19 11:13   10M  
[   ] C_parapsilosis_CDC317_parapsilosis_group_phyloP_scores.wig.gz   2017-12-19 12:28  5.8M  
[SND] C_parapsilosis_CDC317_saccharomycetales.noncons.mod             2017-12-19 13:23  714   
[   ] C_parapsilosis_CDC317_saccharomycetales.tar.gz                  2017-12-19 11:23   26M  
[   ] C_parapsilosis_CDC317_saccharomycetales_phyloP_scores.wig.gz    2017-12-19 12:32  9.2M  

The /download/genome_alignments/C_parapsilosis_CDC317/ directory contains 
whole-genome multiple sequence alignments, conservation scores, and 
phylogenetic models for Candida parapsilosis CDC317.

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. parapsilosis CDC317 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_parapsilosis_CDC317_candida_lodderomyces.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_parapsilosis_CDC317_candida_lodderomyces.tar.gz. The parameters used were: target 
	coverage (gamma) = 0.39, expected element length (omega) = 12.
C_parapsilosis_CDC317_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. parapsilosis CDC317 as reference species, and
	separated into contig-specific files.
C_parapsilosis_CDC317_candida_lodderomyces_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_parapsilosis_CDC317_candida_lodderomyces.tar.gz
C_parapsilosis_CDC317_ctg_clade.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_parapsilosis_CDC317_ctg_clade.tar.gz. The parameters used were: target coverage 
	(gamma) = 0.37, expected element length (omega) = 12.
C_parapsilosis_CDC317_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. parapsilosis CDC317 as reference species, and
	separated into contig-specific files.
C_parapsilosis_CDC317_ctg_clade_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_parapsilosis_CDC317_ctg_clade.tar.gz
C_parapsilosis_CDC317_parapsilosis_group.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_parapsilosis_CDC317_parapsilosis_group.tar.gz. The parameters used were: target coverage 
	(gamma) = 0.44, expected element length (omega) = 12.
C_parapsilosis_CDC317_parapsilosis_group.tar.gz
	Archived and compressed directory containing alignments of the genomes of 3 
	closely-related species: C. parapsilosis CDC317, C. orthopsilosis Co 90-125, 
	and L. elongisporus NRLL YB-4239. The alignments are projected using 
	C. parapsilosis CDC317 as reference species, and separated into contig-specific files.
C_parapsilosis_CDC317_parapsilosis_group_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_parapsilosis_CDC317_parapsilosis_group.tar.gz
C_parapsilosis_CDC317_saccharomycetales.noncons.mod
	Optimized non-conserved phylogenetic model for the alignments in
	C_parapsilosis_CDC317_saccharomycetales.tar.gz. The parameters used were: target 
	coverage (gamma) = 0.36, expected element length (omega) = 12.
C_parapsilosis_CDC317_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. parapsilosis CDC317 as reference species, and
	separated into contig-specific files.
C_parapsilosis_CDC317_saccharomycetales_phyloP_scores.wig.gz
	Conservation scores for the alignments in C_parapsilosis_CDC317_saccharomycetales.tar.gz


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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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