shadow

Usage:

shadow [options] <tree> <alignment>

Description:

Perform phylogenetic shadowing on a given DNA 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 DNA multiple alignment in ClustalW format.

Output:

Shadow will create a directory, named shadow_out by default. Any existing output files in the directory will be overwritten. The directory will contain:

• An XML file named shadow.xml using the CisML schema.
• An HTML file named shadow.html
• A plain text file named shadow.text

The default can be overridden using the --o or --oc options which are described below.

The --text will limit output to plain text sent to the standard output.

Options:

• --bg <float> - The mutation rate for sites in the background model. The default value is 1.
• --bgfile <bfile> - Read background frequencies from <bfile>. The file should be in MEME background file format. The default is to use frequencies embedded in the application from the non-redundant database. If the argument is the keyword motif-file, then the frequencies will be taken from the motif file.
• --fg <float> - The mutation rate for sites in the foreground model(s). The default value is 1.
• --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.
• --list - Treat the second required input as a list of alignments, rather than a single alignment.
• --max-stored-scores <max> - Set the maximum number of scores that will be stored. Precise calculation of q-values depends on having a complete list of scores. However, keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped, and approximate q-values will be calculated. By default the maximum number of stored matches is 100,000.
• --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.
  • 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.

• --no-pvalue - Skip the p-value calculation. This switch will be necessary when a large number n of species are in the tree, because the memory requirement is 4ⁿ. This also disables computation of q-values.
• --no-qvalue - Do not compute a q-value for each p-value. The q-value calculation is that of Benjamini and Hochberg (1995). By default, q-values are computed.
• --o <dir name> - Specifies the output directory. If the directory already exists, the contents will not be overwritten.
• --oc <dir name> - Specifies the output directory. If the directory already exists, the contents will be overwritten.
• --output-pthresh <float> - The p-value threshold for displaying search results. If the p-value of a match is greater than this value, then the match will not be printed. Using the --output-pthresh option will set the q-value threshold to 1.0. The default p-value threshold is 1e-4.
• --output-qthresh <float> - The q-value threshold for displaying search results. If the q-value of a match is greater than this value, then the match will not be printed. Using the --output-qthresh option will set the p-value threshold to 1.0. The default q-value threshold is 1.0.
• --pur-pyr <float> - 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.
• --text Limits output to plain text sent to standard out. For FIMO, the text output is unsorted, and q-values are not reported. This mode allows the program to search an arbitrarily large database, because results are not stored in memory.
• --transition-transversion <float> - 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.
• --verbosity 1|2|3|4 - Set the verbosity of status reports to standard error. The default level is 2.

Warning messages: None