# The MEME Suite

## Motif-based sequence analysis tools

## shadow

### Usage:

`shadow [options] <tree file> <alignment file>`

### 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 File

a phylogenetic tree in Phylip Newick format. This tree may contain additional species not represented in the alignment.

#### Alignment File

A DNA multiple alignment in ClustalW format. Alternatively, if the --list option is used, this file may contain a list of alignment files.

### 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 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.

### Options

Option | Parameter | Description | Default Behaviour
--- | --- | --- | ---
General Options
--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.
Value | Description
--- | ---
skip | Skip those sites where any position in the alignment window contains a gap.
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.
| 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.
Value | Name | Description
--- | --- | ---
single | Single Score | score first sequence: compute standard log-odds score of first sequence in the alignment; ignores tree but does NOT remove gaps.
average | Average Score | compute average of standard log-odds score of aligned sites.
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.
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. | 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. The keyword `motif-file` can be used to indicate that the frequencies should be taken from the motif file. | 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.