RAxML - Revision history

Rf at 12:18, 8 March 2017

2017-03-08T12:18:10Z

Rf at 15:17, 12 January 2017

2017-01-12T15:17:53Z

Jw297: /* Example usage */

2016-12-19T10:40:01Z

‎Example usage

Rf at 15:33, 19 August 2016

2016-08-19T15:33:43Z

Rf at 17:40, 4 August 2016

2016-08-04T17:40:19Z

Rf at 17:38, 4 August 2016

2016-08-04T17:38:11Z

Rf at 14:59, 4 August 2016

2016-08-04T14:59:06Z

Rf at 12:51, 4 August 2016

2016-08-04T12:51:39Z

Rf at 11:47, 4 August 2016

2016-08-04T11:47:55Z

Rf at 11:40, 4 August 2016

2016-08-04T11:40:51Z

← Older revision		Revision as of 12:18, 8 March 2017
Line 63:		Line 63:
	assert(0);		assert(0);
	}		}
		+
		+	= Links =
		+	* [https://academic.oup.com/sysbio/article/50/6/913/1628902/A-Likelihood-Approach-to-Estimating-Phylogeny-from This] is a link to the Paul Lewis paper.

@@ Line 11: / Line 11: @@
 Standard usage
-  raxml -m GTRGAMMA -s <alignment_of_sequences> -n <extension_label_suffixed_to_outputfiles> -t <sequence_alignment_tree>
+  raxml -m GTRGAMMA -s <alignment_of_sequences> -n <extension_label_suffixed_to_outputfiles> -p  -t <sequence_alignment_tree>
 When using SNPs as input, the following command-line will work:
-  raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s <snps_as_fasta_file> -p 12345 -n <extension_label_suffixed_to_outputfiles>
+  raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s <snps_as_fasta_file> -p <your_number_for_random_seed> -n <extension_label_suffixed_to_outputfiles>
 <ins>Explanation</a>:

@@ Line 18: / Line 18: @@
 <ins>Explanation</a>:
-* ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).
+* ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accounts for the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).
 Note: the capital t option "-T" refers to CPUs/threads. This is to be expected though there can be some confusion with the tree option "-t"

@@ Line 19: / Line 19: @@
 <ins>Explanation</a>:
 * ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).
 = Program code =

@@ Line 22: / Line 22: @@
 = Program code =
-Because the ascertainment bias section of the manual is not terribly comprehensive, here is the relevant part of the source for the different types of ascertainment bias:
+Because the ascertainment bias section of the manual is not terribly comprehensive, here is the relevant part of the source ocde (the c module '''evaluateGenericSpecial.c''') for the different types of ascertainment bias:
   correction = evaluateCatAsc(ex1_asc, ex2_asc, x1_start_asc, x2_start_asc, tr->partitionData[model].tipVector,
@@ Line 38: / Line 38: @@
+    }
+  switch(tr->ascertainmentCorrectionType) {
     case LEWIS_CORRECTION:
   partitionLikelihood = partitionLikelihood - (double)w * LOG(1.0 - correction);

← Older revision		Revision as of 17:38, 4 August 2016
Line 19:		Line 19:
	<ins>Explanation</a>:		<ins>Explanation</a>:
	* ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).		* ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).
		+
		+	= Program code =
		+
		+	Because the ascertainment bias section of the manual is not terribly comprehensive, here is the relevant part of the source for the different types of ascertainment bias:
		+
		+	correction = evaluateCatAsc(ex1_asc, ex2_asc, x1_start_asc, x2_start_asc, tr->partitionData[model].tipVector,
		+	tip, ascWidth, diagptable, ascWidth, &accumulator, weightVector, tr->partitionData[model].dataType,
		+	tipNodeNumber, &goldmanAccumulator);
		+	}
		+	break;
		+	case GAMMA:
		+	correction = evaluateGammaAsc(ex1_asc, ex2_asc, x1_start_asc, x2_start_asc, tr->partitionData[model].tipVector,
		+	tip, ascWidth, diagptable, ascWidth, &accumulator, weightVector, tr->partitionData[model].dataType,
		+	tipNodeNumber, &goldmanAccumulator);
		+	break;
		+	default:
		+	assert(0);
		+	}
		+
		+
		+	switch(tr->ascertainmentCorrectionType)
		+	{
		+	case LEWIS_CORRECTION:
		+	partitionLikelihood = partitionLikelihood - (double)w * LOG(1.0 - correction);
		+	break;
		+	case STAMATAKIS_CORRECTION:
		+	partitionLikelihood += accumulator;
		+	break;
		+	case FELSENSTEIN_CORRECTION:
		+	partitionLikelihood += tr->partitionData[model].invariableWeight * LOG(correction);
		+	break;
		+	case GOLDMAN_CORRECTION_1:
		+	partitionLikelihood += ((correction * (double)w * LOG(correction)) / (1.0 - correction));
		+	break;
		+	case GOLDMAN_CORRECTION_2:
		+	//printf("Goldman acc: %f\n", goldmanAccumulator);
		+	partitionLikelihood += (((double)w / (1.0 - correction)) * goldmanAccumulator);
		+	break;
		+	case GOLDMAN_CORRECTION_3:
		+	partitionLikelihood += ((tr->partitionData[model].invariableWeight / correction) * goldmanAccumulator);
		+	break;
		+	default:
		+	assert(0);
		+	}

← Older revision		Revision as of 14:59, 4 August 2016
Line 18:		Line 18:

	<ins>Explanation</a>:		<ins>Explanation</a>:
−	* ASC refers to ascertainment bias.	+	* ASC refers to ascertainment bias (known in the original Paul Lewis paper as acquisition bias) accoutn sfor the fact that all the sites are variable, as opposed to other types of alignments which include all the constant or common characters).

← Older revision		Revision as of 12:51, 4 August 2016
Line 15:		Line 15:
	When using SNPs as input, the following command-line will work:		When using SNPs as input, the following command-line will work:

−	raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s ~~out_report3.fasta~~ -p 12345 -n ~~OR3~~	+	raxmlHPC -m ASC_GTRGAMMA --asc-corr=lewis -s <snps_as_fasta_file> -p 12345 -n <extension_label_suffixed_to_outputfiles>
		+
		+	<ins>Explanation</a>:
		+	* ASC refers to ascertainment bias.