shadow

Usage: shadow [options] <tree> <alignment>

Description:

Perform phylogenetic shadowing on a given alignment, using a given tree (Boffelli et al, Science 2003). This program is a simplified version of motiph, in which the equilibrium distribution is set equal to the background model, rather than being taken from a given motif.

Input:

• <tree> is a phylogenetic tree in Phylip Newick format. This tree may contain additional species not represented in the alignment.
• <alignment> is a multiple alignment in ClustalW format.

Output:

The output is in GFF format with the forward and reverse scores listed as separate features. Scores are p-values derived from log-odds base 2.

Options:

• --gap <method> Specifies the gap handling strategy. Allowed values for method are:
  • skip Skip those sites where any position in the alignment window contains a gap. This is the default gap handling strategy.
  • fixed Sites containing gaps are assigned a fixed score, specified by --gap-cost.
  • wildcard The gap character matches any base, and the score is the product of the corresponding probabilities.
  • minimum The gap character is assigned the score corresponding to the least likely letter at the given position.
  • model Use model-specific gap handling. Currently, the only model that supports this is f81_gap.
• --gap-cost <float> Specifies the costs for gaps when using the fixed gap handling strategy. Default is 0.0.
• --gap-freq <float> Specifies the background frequency for gaps. Default is derived from the alignment.
• --bgfile <background file> The name of a file specifying background frequencies for each of the nucleotides.
• --fg <value> The mutation rate for sites in the foreground model. The default value is 1.
• --bg <value> The mutation rate for sites in the background model. The default value is 1.
• --model [jc|k2|f81|f84|hky|tn] The evolutionary model to use. The available models are:
  • jc - Jukes-Cantor: equilibrium base frequencies are all 1/4; the only free parameter is the mutation rate.
  • k2 - Kimura 2-parameter: equilibrium base frequencies are all 1/4; the free parameters are the mutation rate and the transition/transversion rate ratio.
  • f81 - Felsenstein 1981: equilibrium base frequencies are taken from the alignment; the only free parameter is the mutation rate.
  • f81_gap - Identical to f81 but treats gaps as an additional symbol in the alphabet.
  • f84 - Felsenstein 1984: equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate and the transition/transversion rate ratio. The ratio of purine-purine to pyrimidine->pyrimidine transitions is assumed to be 1.
  • hky - Hasegawa-Kishino-Yano: equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate and the transition/transversion rate ratio. The ratio of purine-purine to pyrimidine-pyrimidine transitions is assumed to be equal to the ratio of purines to pyrimidines.
  • tn - Tamura-Nei: equilibrium base frequencies are taken from the alignment; the free parameters are the mutation rate, the transition/transversion rate ratio, and the ratio of purine-purine transitions to pyrimidine-pyrimidine transitions.
  The default model is f81. A description of the f81 model is available in chapter 13 of Statistical Methods in Bioinformatics by Ewens and Grant. The other models are described in chapters 9 and 13 of Inferring Phylogenies by Felsenstein.
• --r <value> The ratio of the purine transition rate to pyrimidine transition rate. This parameter is used by the Tamura-nei model. The default value is 1.0.
• --R <value> The ratio of the transition rate to the transversion rate. This parameter is used by the Kimura 2-parameter, F84, HKY, and Tamura-nei models. The default value is 0.5.
• --sequence-name <string> The sequence ID to appear in column one of the output. The default value is "<file name>.<sequence ID>", where "<file name>" is the name of the alignment file and "<sequence ID>" is the ID of the first sequence in the alignment.
• --pseudocounts <float> A pseudocount to be added to each count in the motif matrix, weighted by the background frequencies for the nucleotides (Dirichlet prior), before converting the motif to probabilities. The default value is 0.1.
• --verbosity [1|2|3|4|5|6] Set the verbosity of status reports to standard error. The default value is 2.

Warning messages: None

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