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