shadow [options] <tree file> <alignment file>
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.
a phylogenetic tree in Phylip Newick format. This tree may contain additional species not represented in the alignment.
A DNA multiple alignment in ClustalW format. Alternatively, if the --list option is used, this file may contain a list of alignment files.
Shadow will create a directory, named
shadow_out by default.
Any existing output files in the directory will be overwritten.
The directory will contain:
shadow.xmlusing the CisML schema.
The output directory can be changed using the --o or --oc options which are described below.
The --text will limit output to plain text sent to the standard output.
|--bg||rate||The mutation rate for sites in the background model.||The background mutation rate is set to 1.|
|--fg||rate||The mutation rate for sites in the foreground model(s).||The mutation rate is set to 1.|
|-gap||skip|fixed|wildcard|minimum||Specifies the gap handling strategy.
|Gaps are skipped.|
|--gap-cost||cost||Specifies the costs for gaps when using the fixed gap handling strategy.||The gap cost is zero.|
|--list||Treat the second required input as a list of alignments, rather than a single alignment.||The second required input is a single alignment.|
|--model||single|average|jc|k2|f81|f84|hky|tn||The evolutionary model to use.
|Behaves as if --model f81 was specified.|
|--pur-pyr||ratio||The ratio of the purine transition rate to pyrimidine transition rate. This parameter is used by the Tamura-nei model.||The ratio is set to 1.0.|
|--transition-transversion||ratio||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 ratio is set to 0.5.|
|--bgfile||The file should be in MEME background file format.
||Use the alignment frequencies.|
|--max-stored-scores||count||Set the maximum number of scores that will be stored. 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. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate.||The maximum number of stored matches is 100,000.|
|--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.||The p-values are calculated.|
|--no-qvalue||Do not compute a q-value for each p-value. The q-value calculation is that of Benjamini and Hochberg (1995).||The q-values are calculated.|
|--output-pthresh||p-value threshold||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. If both the --output-pthresh and --output-qthresh options appear on the command line, whichever appears later on the command line will be applied.||The p-value threshold is set to 1e-4.|
|--output-qthresh||q-value threshold||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.||No q-value threshold is applied.|
|--text||Limits output to plain text sent to standard out. For shadow, 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.||Outputs are created as normal.|