Pancrustacean MegaTree - Revision history

128.111.227.71: /* Amino Acids */

2012-07-06T02:07:38Z

‎Amino Acids

2012-07-04T03:59:13Z

‎Regier 62-gene protein coding

2012-07-04T03:57:18Z

‎Concatenated Genomic Files

2012-07-04T03:53:56Z

‎Data Sets

2012-07-04T03:53:01Z

‎EST

2012-07-04T03:52:18Z

‎Full Genomes

2012-07-04T03:46:29Z

‎Full Genomes

2012-07-04T03:41:47Z

‎EST

2012-07-04T03:41:28Z

‎EST

2012-07-04T03:41:13Z

‎New 454

@@ Line 84: / Line 84: @@
      Agriosphodrus_dohrni	COII
      Agriosphodrus_dohrni	COIII
 ====Nucleotide Data====

← Older revision		Revision as of 03:59, 4 July 2012
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	===Regier 62-gene protein coding===		===Regier 62-gene protein coding===
		+	* Regier data were downloaded from supplementary material
		+	* All Regier data were treated as ESTs and combined with the GenBank EST data
		+	* Overlapping taxa between Genbank EST and Regier data were combined into a single fasta files

	===Concatenated Genomic Files===		===Concatenated Genomic Files===

← Older revision		Revision as of 03:57, 4 July 2012
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	===Concatenated Genomic Files===		===Concatenated Genomic Files===
		+	* Phytab CDS and protein files from 454, EST and Genome data were concatenated tail-to-head
		+	* Concatenated Protein data were then aligned using Phytab MUSCLE, while CDS data were aligned using Phytab Prank
		+	* All files (raw and aligned) are available here:
		+	http://knot.cnsi.ucsb.edu:8080/u/marko/h/phytab-ready-arthropod

	===6-gene Data Set===		===6-gene Data Set===

@@ Line 37: / Line 37: @@
 ===Regier 62-gene protein coding===
 ===6-gene Data Set===
 * Seth compiled the 6-gene data set. He sent a file to THO and others on May 15 in an email entitled: Final files: MTrDNA, MTproteom, six gene data set. There were minor changes and a new file sent May 16. THO found a few duplications, including: Nebalia histone, Nebalia 18S, Pollicipes_polymerus

@@ Line 4: / Line 4: @@
 ===EST===
 * All available EST datasets were downloaded directly from genbank
-* See full directory of raw data files here[http://macroevolution.lifesci.ucsb.edu/IlluminaData/PanCrustacea/AnalysisDatasets/ESTsGenBankRegier/]
+* See full directory of raw data files here:
 * All EST data were analyzed using iAssembler. Following iAssembler, orthologs were pulled from the EST data using Hamster (arthNreg2 i.e. hamster orthologs + Regier orthologs)
 * Respective CDS and protein data were concatenated tail-to-head

@@ Line 25: / Line 25: @@
 ===Full Genomes===
 * All available genomic CDS data was downloaded from respective servers (Genbank, wormbase, flybase etc)
 * For versions of the genomes check fasta files
 * All raw data is available here:
 http://macroevolution.lifesci.ucsb.edu/IlluminaData/PanCrustacea/AnalysisDatasets/GenomesCDS/
 ===Regier 62-gene protein coding===

@@ Line 7: / Line 7: @@
 * All EST data were analyzed using iAssembler. Following iAssembler, orthologs were pulled from the EST data using Hamster (arthNreg2 i.e. hamster orthologs + Regier orthologs)
 * Respective CDS and protein data were concatenated tail-to-head
-See results here:
+* See results here:
 http://knot.cnsi.ucsb.edu:8080/u/marko/h/estsgenbankregier