### RepeatMasker annotation file format

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Example of the tab-delimited structure found in .out files.

```text
   SW   perc perc perc  query     position in query      matching       position in repeat
  score div. del. ins.  sequence  begin   end   (left)   repeat         class/family      begin  end (left)   ID

  1355  21.4  4.4  2.3  chr1     1001   1412 (248954211) + L2a          LINE/L2             2401 2811  (615)   1
  1289  19.1  4.6  0.0  chr1     5635   6003 (248949620) C AluSx1       SINE/Alu             (1)  313     1     2
   362  27.4  1.5  3.9  chr1     7126   7268 (248948355) + MIR3         SINE/MIR               1  137   (30)   3
```

--------------------------------

### Configure and Initialize TextResizeDetector

Source: https://github.com/dfam-consortium/repeatmasker/blob/master/HTMLAnnotHeader.html

Setup logic for the detector to monitor specific elements and trigger resize callbacks.

```javascript
TextResizeDetector.TARGET_ELEMENT_ID = 'doc';
TextResizeDetector.USER_INIT_FUNC = null;
// Setup the font-resize listener
function init() {
	var iBase = TextResizeDetector.addEventListener(onFontResize,null);
}
function onFontResize(e,args) {
	adjustRepeatTableWidth();
}
//id of element to check for and insert control
TextResizeDetector.TARGET_ELEMENT_ID = 'repeatTable';
//function to call once TextResizeDetector has init'd
TextResizeDetector.USER_INIT_FUNC = init;
```

--------------------------------

### RepeatMasker summary table format

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Example of the statistical summary output in .tbl files.

```text
==================================================
file name: mygenome.fa
sequences:            1
total length:    152192 bp (148791 bp excl N-runs)
GC level:         39.59 %
bases masked:     88734 bp ( 59.64 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:              195        45195 bp    30.37 %
      ALUs          178        43249 bp    29.07 %
      MIRs           17         1946 bp     1.31 %

LINEs:               54        31173 bp    20.95 %
      LINE1          36        24602 bp    16.53 %
      LINE2          18         6571 bp     4.42 %
```

--------------------------------

### Generate summary statistics with buildSummary.pl

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Creates statistical tables summarizing repeat content from RepeatMasker output files.

```bash
# Generate summary for a genome
./util/buildSummary.pl -species human mygenome.fa.out > summary.tbl

# Combine multiple output files
./util/buildSummary.pl -species mouse chr*.out > genome_summary.tbl
```

--------------------------------

### Visualize repeat landscapes with createRepeatLandscape.pl

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Generates HTML or JavaScript visualizations of repeat family distribution by divergence level.

```bash
# Create landscape with known genome size
./util/createRepeatLandscape.pl -div mygenome.divsum -g 3100000000 > landscape.html

# Use twoBit file to calculate genome size automatically
./util/createRepeatLandscape.pl -div mygenome.divsum \
    -twoBit mygenome.2bit \
    -t "Human Repeat Landscape" > human_landscape.html

# Output JavaScript only (for embedding)
./util/createRepeatLandscape.pl -div mygenome.divsum -g 2800000000 -j > landscape.js
```

--------------------------------

### Run RepeatMasker and Analyze Results

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

This sequence of commands outlines the process of running RepeatMasker on a genome, calculating divergence statistics from the alignment, creating a repeat landscape visualization, and converting the output to GFF3 format for genome browsers.

```bash
RepeatMasker -species human -pa 32 -s -a -gff -dir results genome.fa
```

```bash
./util/calcDivergenceFromAlign.pl \
    -s results/genome.divsum \
    results/genome.fa.align.gz
```

```bash
./util/createRepeatLandscape.pl \
    -div results/genome.divsum \
    -twoBit genome.2bit \
    -t "Genome Repeat Landscape" > results/landscape.html
```

```bash
./util/rmOutToGFF3.pl results/genome.fa.out > results/repeats.gff3
```

--------------------------------

### Convert RepeatMasker output to BED with RM2Bed.py

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Converts RepeatMasker output to BED format for UCSC track hubs.

```bash
# Basic conversion to BED format
python util/RM2Bed.py mygenome.fa.out

# Generate BigBed files for track hub
python util/RM2Bed.py -d output_dir -b mygenome.fa.out
```

--------------------------------

### Cross-Species Alignment Preparation with RepeatMasker

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

This workflow prepares sequences for cross-species alignment by masking lineage-specific repeats. It involves an initial RepeatMasker run, followed by annotation of lineage-specific versus ancestral repeats using the DateRepeats tool.

```bash
RepeatMasker -species human -pa 16 -a human_chr1.fa
```

```bash
DateRepeats human_chr1.fa.out -query human -comp mouse -mask mouse
```

--------------------------------

### Apply masking with maskFile.pl

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Applies repeat masking to a sequence file based on a RepeatMasker output file.

```bash
# Mask sequences using annotation file
./util/maskFile.pl -annotations mygenome.fa.out -fasta mygenome.fa > masked.fa

# Soft-mask (lowercase) instead of hard-mask
./util/maskFile.pl -annotations mygenome.fa.out -fasta mygenome.fa -softmask > softmasked.fa
```

--------------------------------

### Implement TextResizeDetector Utility

Source: https://github.com/dfam-consortium/repeatmasker/blob/master/HTMLAnnotHeader.html

A JavaScript singleton that detects browser font size changes and fires custom events.

```javascript
/**
 * @fileoverview TextResizeDetector
 *
 * Detects changes to font sizes when user changes browser settings
 * <br>Fires a custom event with the following data:<br><br>
 * iBase : base font size
 * iDelta : difference in pixels from previous setting<br>
 * iSize : size in pixel of text<br>
 *
 *
 * @author Lawrence Carvalho carvalho@uk.yahoo-inc.com
 * @version 1.0
 */
/**
 * @constructor
 */
TextResizeDetector = function() {
	var el = null;
	var iIntervalDelay = 200;
	var iInterval = null;
	var iCurrSize = -1;
	var iBase = -1;
	var aListeners = [];
	var createControlElement = function() {
		el = document.createElement('span');
		el.id='textResizeControl';
		el.innerHTML='&nbsp;';
		el.style.position="absolute";
		el.style.left="-9999px";
		var elC = document.getElementById(TextResizeDetector.TARGET_ELEMENT_ID);
		// insert before firstChild
		if (elC) elC.insertBefore(el,elC.firstChild);
		iBase = iCurrSize = TextResizeDetector.getSize();
	};
	function _stopDetector() {
		window.clearInterval(iInterval);
		iInterval=null;
	};
	function _startDetector() {
		if (!iInterval) {
			iInterval = window.setInterval('TextResizeDetector.detect()', iIntervalDelay);
		}
	};
	function _detect() {
		var iNewSize = TextResizeDetector.getSize();
		if(iNewSize!== iCurrSize) {
			for (var i=0;i <aListeners.length;i++) {
				aListnr = aListeners[i];
				var oArgs = { iBase: iBase,iDelta:((iCurrSize!=-1) ? iNewSize - iCurrSize + 'px' : "0px"),iSize:iCurrSize = iNewSize};
				if (!aListnr.obj) {
					aListnr.fn('textSizeChanged',[oArgs]);
				} else {
					aListnr.fn.apply(aListnr.obj,['textSizeChanged',[oArgs]]);
				}
			}
		}
		return iCurrSize;
	};
	var onAvailable = function() {
		if (!TextResizeDetector.onAvailableCount_i ) {
			TextResizeDetector.onAvailableCount_i =0;
		}
		if (document.getElementById(TextResizeDetector.TARGET_ELEMENT_ID)) {
			TextResizeDetector.init();
			if (TextResizeDetector.USER_INIT_FUNC){
				TextResizeDetector.USER_INIT_FUNC();
			}
			TextResizeDetector.onAvailableCount_i = null;
		} else {
			if (TextResizeDetector.onAvailableCount_i<600) {
				TextResizeDetector.onAvailableCount_i++;
				setTimeout(onAvailable,200)
			}
		}
	};
	setTimeout(onAvailable,500);
	return {
		/*
		 * Initializes the detector
		 *
		 * @param {String} sId The id of the element in which to
		 * create the control element
		 */
		init: function() {
			createControlElement();
			_startDetector();
		},
		/**
		 * Adds listeners to the ontextsizechange event.
		 * Returns the base font size
		 *
		 */
		addEventListener:function(fn,obj,bScope) {
			aListeners[aListeners.length] = { fn: fn, obj: obj }
			return iBase;
		},
		/**
		 * performs the detection and fires textSizeChanged event
		 * @return the current font size
		 * @type {integer}
		 */
		detect:function() {
			return _detect();
		},
		/**
		 * Returns the height of the control element
		 *
		 * @return the current height of control element
		 * @type {integer}
		 */
		getSize:function() {
			var iSize;
			return el.offsetHeight;
		},
		/**
		 * Stops the detector
		 */
		stopDetector:function() {
			return _stopDetector();
		},
		/*
		 * Starts the detector
		 */
		startDetector:function() {
			return _startDetector();
		}
	}
}();
```

--------------------------------

### Manage UI Elements and Table Layout

Source: https://github.com/dfam-consortium/repeatmasker/blob/master/HTMLAnnotHeader.html

Functions to toggle visibility of elements and dynamically adjust table widths.

```javascript
// Setup the table expansion/collapse handler
function toggleDiv(divid){
	if(document.getElementById(divid).style.display == 'none'){
		document.getElementById(divid).style.display = 'block';
	}else{
		document.getElementById(divid).style.display = 'none';
	}
}
// Setup the table resize method
function adjustRepeatTableWidth() {
	var numInsertionLevels = 3;
	var pixelPaddingPerLevel = 10;
	var objColHeaderText = document.getElementById("colHeaderText");
	if ( objColHeaderText != null ) {
		var newWidth = objColHeaderText.offsetWidth + ( pixelPaddingPerLevel * (numInsertionLevels - 1) ) + 30;
		document.getElementById("repeatTable").style.width = newWidth + "px";
	}
}
function toggleAllHsps() {
	var idx = 1;
	while( document.get
```

--------------------------------

### famdb.py: Querying the FamDB Repeat Database

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Utility to query the FamDB repeat database for information on taxonomy, repeat families, and lineage. Supports various output formats including JSON and pretty-printed trees.

```bash
# Display database information and statistics
./famdb.py -i Libraries/famdb info
```

```bash
# Display database info with history
./famdb.py -i Libraries/famdb info --history
```

```bash
# Search for species names matching a term
./famdb.py -i Libraries/famdb names "homo sapiens"
```

```bash
./famdb.py -i Libraries/famdb names mouse --format json
```

```bash
# Show lineage with ancestor and descendant counts
./famdb.py -i Libraries/famdb lineage --ancestors --descendants human --format totals
```

```bash
# Display full taxonomic lineage tree
./famdb.py -i Libraries/famdb lineage --ancestors --descendants "mus musculus" --format pretty
```

```bash
# Export families for a species in FASTA format
./famdb.py -i Libraries/famdb families \
    --format fasta_name \
    --ancestors --descendants 'homo sapiens' \
    --include-class-in-name
```

```bash
# Export HMM profiles for a species
./famdb.py -i Libraries/famdb families \
    --format hmm \
    --ancestors --descendants 'drosophila' \
    --curated-only
```

```bash
# Get information about a specific family
./famdb.py -i Libraries/famdb family --format summary DF0000001
```

--------------------------------

### Convert RepeatMasker output to GFF3 with rmOutToGFF3.pl

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Transforms RepeatMasker .out files into GFF3 format for compatibility with genome browsers.

```bash
# Convert OUT file to GFF3
./util/rmOutToGFF3.pl mygenome.fa.out > mygenome_repeats.gff3

# Convert multiple files
./util/rmOutToGFF3.pl *.out > all_repeats.gff3
```

--------------------------------

### Calculate divergence with calcDivergenceFromAlign.pl

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Computes CpG-adjusted Kimura divergence values from RepeatMasker alignment files for landscape plotting.

```bash
# Generate divergence summary for landscape creation
./util/calcDivergenceFromAlign.pl -s mygenome.divsum mygenome.fa.align.gz

# Generate both summary and new alignment file with divergence values
./util/calcDivergenceFromAlign.pl -s mygenome.divsum \
    -a mygenome_with_div.align \
    mygenome.fa.align.gz

# Calculate standard Kimura without CpG modification
./util/calcDivergenceFromAlign.pl -noCpGMod -s mygenome.divsum mygenome.fa.align
```

--------------------------------

### Define CSS Styles for Annotations

Source: https://github.com/dfam-consortium/repeatmasker/blob/master/HTMLAnnotHeader.html

Styles for annotation sets and report-style alternating line backgrounds.

```css
.annotSet { /* Annotation Set - A grouping which spans a complete set of linked annotations. */ border-right: 1px solid; padding-right: 10px; } .bluediv { /* The style for every other line. Used to create a report effect */ background: url("bluegrad.jpg")top right repeat-y; background-color: #bacdff; margin-bottom: 5px; margin-top: 5px; } pre { /* Required change in pre formatting. This fixes problems with spacing inside of annotSet div tags */ margin: 0px 0px 0px 0px; font-family: monospace; } .nound { font-weight:bold; color:navy; text-decoration:none; }
```

--------------------------------

### RepeatMasker: Basic Sequence Masking

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Use this command to mask repetitive DNA in FASTA files for a specified species. Supports parallel processing and different search engines.

```bash
# Basic usage - mask a sequence file for human
RepeatMasker -species human mysequence.fa
```

```bash
# Quick search with parallel processing (16 parallel jobs)
RepeatMasker -species mouse -pa 16 -q genome.fa
```

```bash
# Sensitive search with RMBlast engine
RepeatMasker -species "drosophila melanogaster" -s -e rmblast genome.fa
```

```bash
# Use custom library instead of species database
RepeatMasker -lib custom_repeats.fa -cutoff 250 mysequence.fa
```

```bash
# Generate alignments and GFF output, mask with lowercase
RepeatMasker -species human -a -gff -xsmall chromosome1.fa
```

```bash
# Mask only low complexity DNA, skip interspersed repeats
RepeatMasker -noint mysequence.fa
```

```bash
# Mask only Alus (primate-specific)
RepeatMasker -species human -alu -div 10 mysequence.fa
```

```bash
# Specify output directory and use HMMER engine
RepeatMasker -species arabidopsis -e hmmer -dir ./results mygenome.fa
```

--------------------------------

### Annotate segmental duplications with DupMasker

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Use DupMasker to identify segmental duplications in genomic sequences. Supports engine selection, parallel processing, and custom filtering parameters.

```bash
# Basic usage - annotate segmental duplications
DupMasker mysequence.fa

# Use specific search engine with parallel processing
DupMasker -engine rmblast -pa 8 chromosome1.fa

# Generate alignments and GFF output
DupMasker -align -gff mygenome.fa

# Filter by divergence and set maximum gap width
DupMasker -maxDiv 10 -maxWidth 500 mysequence.fa

# Force re-search even if previous results exist
DupMasker -forceSearch chromosome1.fa
```

--------------------------------

### Toggle HSP Visibility Functions

Source: https://github.com/dfam-consortium/repeatmasker/blob/master/HTMLAnnotHeader.html

Functions to iterate through document elements with IDs prefixed by 'hsps' to modify their display style.

```javascript
ElementById('hsps'+idx) != null ) { toggleDiv( 'hsps'+idx ); idx++; } return false; } function openAllHsps(){ var idx = 1; while( document.getElementById('hsps'+idx) != null ) { document.getElementById('hsps'+idx).style.display = 'block'; idx++; } return false; } function closeAllHsps(){ var idx = 1; while( document.getElementById('hsps'+idx) != null ) { document.getElementById('hsps'+idx).style.display = 'none'; idx++; } return false; }
```

--------------------------------

### DateRepeats: Lineage-Specific Repeat Annotation

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Annotate the lineage specificity of repeats for cross-species genomic alignment preparation. Supports aggressive masking and exclusion of simple repeats.

```bash
# Basic comparison - annotate mouse repeats vs rat and human
DateRepeats mouse_genome.fa.out -query mouse -comp rat -comp human
```

```bash
# Create masked sequence for alignment against rat
DateRepeats mouse_genome.fa.out -query mouse -comp rat -mask rat
```

```bash
# Aggressive masking, including uncertain assignments
DateRepeats human_chr1.fa.out -query human -comp mouse -mask mouse -aggressive
```

```bash
# Skip masking of simple repeats and low complexity
DateRepeats genome.fa.out -query rat -comp mouse -mask mouse -nolow
```

--------------------------------

### ProcessRepeats: Post-Processing RepeatMasker Output

Source: https://context7.com/dfam-consortium/repeatmasker/llms.txt

Refine RepeatMasker annotations by merging fragments, assigning IDs, and generating summary statistics. Supports GFF output and exclusion of specific repeat types.

```bash
# Basic usage - reprocess annotation with species-specific adjustments
ProcessRepeats -species mouse mysequence.fa.cat
```

```bash
# Generate GFF output and exclude simple repeats from display
ProcessRepeats -species human -gff -nolow mygenome.fa.cat
```

```bash
# Generate polymorphic repeat list and alignment file
ProcessRepeats -species rat -poly -a mysequence.fa.cat
```

```bash
# Exclude N-runs from density calculations (useful for draft assemblies)
ProcessRepeats -species human -excln draft_genome.fa.cat
```

```bash
# Mask the source sequence using the annotation
ProcessRepeats -species cow -maskSource mygenome.fa -xsmall mygenome.fa.cat
```

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