1<h2><a name="See also">See also</a></h2> 2<table border cellpadding=4 bgcolor="#FFFFF0"> 3<tr><th>Program name</th> 4<th>Description</th></tr> 5<tr> 6<td><a href="aligncopy.html">aligncopy</a></td> 7<td>Read and write alignments</td> 8</tr> 9 10<tr> 11<td><a href="aligncopypair.html">aligncopypair</a></td> 12<td>Read and write pairs from alignments</td> 13</tr> 14 15<tr> 16<td><a href="biosed.html">biosed</a></td> 17<td>Replace or delete sequence sections</td> 18</tr> 19 20<tr> 21<td><a href="codcopy.html">codcopy</a></td> 22<td>Copy and reformat a codon usage table</td> 23</tr> 24 25<tr> 26<td><a href="cutseq.html">cutseq</a></td> 27<td>Remove a section from a sequence</td> 28</tr> 29 30<tr> 31<td><a href="degapseq.html">degapseq</a></td> 32<td>Remove non-alphabetic (e.g. gap) characters from sequences</td> 33</tr> 34 35<tr> 36<td><a href="descseq.html">descseq</a></td> 37<td>Alter the name or description of a sequence</td> 38</tr> 39 40<tr> 41<td><a href="entret.html">entret</a></td> 42<td>Retrieve sequence entries from flatfile databases and files</td> 43</tr> 44 45<tr> 46<td><a href="extractalign.html">extractalign</a></td> 47<td>Extract regions from a sequence alignment</td> 48</tr> 49 50<tr> 51<td><a href="extractfeat.html">extractfeat</a></td> 52<td>Extract features from sequence(s)</td> 53</tr> 54 55<tr> 56<td><a href="extractseq.html">extractseq</a></td> 57<td>Extract regions from a sequence</td> 58</tr> 59 60<tr> 61<td><a href="featcopy.html">featcopy</a></td> 62<td>Read and write a feature table</td> 63</tr> 64 65<tr> 66<td><a href="featmerge.html">featmerge</a></td> 67<td>Merge two overlapping feature tables</td> 68</tr> 69 70<tr> 71<td><a href="featreport.html">featreport</a></td> 72<td>Read and write a feature table</td> 73</tr> 74 75<tr> 76<td><a href="feattext.html">feattext</a></td> 77<td>Return a feature table original text</td> 78</tr> 79 80<tr> 81<td><a href="makenucseq.html">makenucseq</a></td> 82<td>Create random nucleotide sequences</td> 83</tr> 84 85<tr> 86<td><a href="makeprotseq.html">makeprotseq</a></td> 87<td>Create random protein sequences</td> 88</tr> 89 90<tr> 91<td><a href="maskambignuc.html">maskambignuc</a></td> 92<td>Mask all ambiguity characters in nucleotide sequences with N</td> 93</tr> 94 95<tr> 96<td><a href="maskambigprot.html">maskambigprot</a></td> 97<td>Mask all ambiguity characters in protein sequences with X</td> 98</tr> 99 100<tr> 101<td><a href="maskfeat.html">maskfeat</a></td> 102<td>Write a sequence with masked features</td> 103</tr> 104 105<tr> 106<td><a href="maskseq.html">maskseq</a></td> 107<td>Write a sequence with masked regions</td> 108</tr> 109 110<tr> 111<td><a href="newseq.html">newseq</a></td> 112<td>Create a sequence file from a typed-in sequence</td> 113</tr> 114 115<tr> 116<td><a href="nohtml.html">nohtml</a></td> 117<td>Remove mark-up (e.g. HTML tags) from an ASCII text file</td> 118</tr> 119 120<tr> 121<td><a href="noreturn.html">noreturn</a></td> 122<td>Remove carriage return from ASCII files</td> 123</tr> 124 125<tr> 126<td><a href="nospace.html">nospace</a></td> 127<td>Remove whitespace from an ASCII text file</td> 128</tr> 129 130<tr> 131<td><a href="notab.html">notab</a></td> 132<td>Replace tabs with spaces in an ASCII text file</td> 133</tr> 134 135<tr> 136<td><a href="notseq.html">notseq</a></td> 137<td>Write to file a subset of an input stream of sequences</td> 138</tr> 139 140<tr> 141<td><a href="nthseq.html">nthseq</a></td> 142<td>Write to file a single sequence from an input stream of sequences</td> 143</tr> 144 145<tr> 146<td><a href="nthseqset.html">nthseqset</a></td> 147<td>Read and write (return) one set of sequences from many</td> 148</tr> 149 150<tr> 151<td><a href="pasteseq.html">pasteseq</a></td> 152<td>Insert one sequence into another</td> 153</tr> 154 155<tr> 156<td><a href="revseq.html">revseq</a></td> 157<td>Reverse and complement a nucleotide sequence</td> 158</tr> 159 160<tr> 161<td><a href="seqcount.html">seqcount</a></td> 162<td>Read and count sequences</td> 163</tr> 164 165<tr> 166<td><a href="seqret.html">seqret</a></td> 167<td>Read and write (return) sequences</td> 168</tr> 169 170<tr> 171<td><a href="seqretsetall.html">seqretsetall</a></td> 172<td>Read and write (return) many sets of sequences</td> 173</tr> 174 175<tr> 176<td><a href="seqretsplit.html">seqretsplit</a></td> 177<td>Read sequences and write them to individual files</td> 178</tr> 179 180<tr> 181<td><a href="sizeseq.html">sizeseq</a></td> 182<td>Sort sequences by size</td> 183</tr> 184 185<tr> 186<td><a href="skipredundant.html">skipredundant</a></td> 187<td>Remove redundant sequences from an input set</td> 188</tr> 189 190<tr> 191<td><a href="skipseq.html">skipseq</a></td> 192<td>Read and write (return) sequences, skipping first few</td> 193</tr> 194 195<tr> 196<td><a href="splitsource.html">splitsource</a></td> 197<td>Split sequence(s) into original source sequences</td> 198</tr> 199 200<tr> 201<td><a href="splitter.html">splitter</a></td> 202<td>Split sequence(s) into smaller sequences</td> 203</tr> 204 205<tr> 206<td><a href="trimest.html">trimest</a></td> 207<td>Remove poly-A tails from nucleotide sequences</td> 208</tr> 209 210<tr> 211<td><a href="trimseq.html">trimseq</a></td> 212<td>Remove unwanted characters from start and end of sequence(s)</td> 213</tr> 214 215<tr> 216<td><a href="trimspace.html">trimspace</a></td> 217<td>Remove extra whitespace from an ASCII text file</td> 218</tr> 219 220<tr> 221<td><a href="union.html">union</a></td> 222<td>Concatenate multiple sequences into a single sequence</td> 223</tr> 224 225<tr> 226<td><a href="vectorstrip.html">vectorstrip</a></td> 227<td>Remove vectors from the ends of nucleotide sequence(s)</td> 228</tr> 229 230<tr> 231<td><a href="yank.html">yank</a></td> 232<td>Add a sequence reference (a full USA) to a list file</td> 233</tr> 234 235</table> 236