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comparison mafft.xml @ 7:aaefa93c2dd2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
author rnateam
date Wed, 15 Apr 2020 15:33:37 -0400
parents 15974dd17515
children 4de39704d423
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6:c5908940967d 7:aaefa93c2dd2
1 <tool id="rbc_mafft" name="MAFFT" version="7.221.3"> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <description>Multiple alignment program for amino acid or nucleotide sequences</description> 2 <tool id="rbc_mafft" name="MAFFT" version="@TOOL_VERSION@+galaxy@VERSION@">
3 <requirements> 3 <description>Multiple alignment program for amino acid or nucleotide sequences</description>
4 <requirement type="package" version="7.221">mafft</requirement> 4 <macros>
5 </requirements> 5 <import>macros.xml</import>
6 <stdio> 6 </macros>
7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 7 <expand macro="requirements" />
8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 8 <stdio>
9 </stdio> 9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
10 <version_command> 10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
11 </stdio>
12 <version_command> <![CDATA[
13 mafft --version
14 ]]>
15 </version_command>
16 <command>
11 <![CDATA[ 17 <![CDATA[
12 mafft --version 18
19 #if $cond_flavour.flavourType == 'custom'
20 #if $cond_flavour.dist_flavour.distance_method == '--fastapair'
21 export FASTA_4_MAFFT=`which fasta36`;
22 #end if
23 #end if
24
25 #if $cond_flavour.flavourType != 'custom'
26 $cond_flavour.flavourType
27 #elif $cond_flavour.flavourType == 'custom'
28 ### full parameter options
29 mafft
30 $cond_flavour.dist_flavour.distance_method
31 #if $cond_flavour.dist_flavour.distance_method == '--6merpair'
32 --retree $cond_flavour.dist_flavour.retree
33 $cond_flavour.dist_flavour.distance_method.usetree.parttree
34
35 #if $cond_flavour.dist_flavour.distance_method.usetree.parttree==--parttree
36 $cond_flavour.dist_flavour.distance_method.usetree.treedistance
37 $cond_flavour.dist_flavour.distance_method.usetree.partsize
38 $cond_flavour.dist_flavour.distance_method.usetree.groupsize
39 #end if
40
41 #elif $cond_flavour.dist_flavour.distance_method == '--globalpair'
42 --weighti $cond_flavour.dist_flavour.weighti
43 #elif $cond_flavour.dist_flavour.distance_method == '--localpair'
44 --weighti $cond_flavour.dist_flavour.weighti
45 --lop $cond_flavour.dist_flavour.lop
46 --lep $cond_flavour.dist_flavour.lep
47 --lexp $cond_flavour.dist_flavour.lexp
48 #elif $cond_flavour.dist_flavour.distance_method == '--genafpair'
49 --weighti $cond_flavour.dist_flavour.weighti
50 --lop $cond_flavour.dist_flavour.lop
51 --lep $cond_flavour.dist_flavour.lep
52 --lexp $cond_flavour.dist_flavour.lexp
53 --LOP $cond_flavour.dist_flavour.skipLOP
54 --EXP $cond_flavour.dist_flavour.skipEXP 1
55 #elif $cond_flavour.dist_flavour.distance_method == '--fastapair'
56 --weighti $cond_flavour.dist_flavour.weighti
57 #end if
58 --maxiterate $cond_flavour.iterations
59 $cond_flavour.fft
60 $cond_flavour.score
61 #end if
62
63 ## specify threads to use
64 --thread \${GALAXY_SLOTS:-1}
65 $datatype
66 --ep $ep
67 --op $op
68
69 #if $matrix_condition.matrix == "BLOSUM"
70 --bl $matrix_condition.BLOSUM
71 #elif $matrix_condition.matrix == "PAM"
72 --jtt $matrix_condition.PAM
73 --tm $matrix_condition.tm
74 #elif $matrix_condition.matrix == "custom"
75 --aamatrix '$matrix_condition.matrixfile'
76 --fmodel $matrix_condition.fmodel
77 #end if
78
79 $reorder
80 $getTree
81 $outputFormat
82 '$inputSequences' > '$outputAlignment';
83
84 #if $getTree == "--treeout"
85 mv '${inputSequences}.tree' '$outputTree';
86 #end if
13 ]]> 87 ]]>
14 </version_command> 88 </command>
15 <command> 89 <inputs>
16 <![CDATA[ 90 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
17 #if $cond_flavour.flavourType != 'custom' 91 <param name="datatype" type="select" label="Data type">
18 $cond_flavour.flavourType 92 <option value="">Auto detection</option>
19 #elif $cond_flavour.flavourType == 'custom' 93 <option value="--nuc">Nucleic acids</option>
20 ### full parameter options 94 <option value="--amino">Amino acids</option>
21 mafft 95 </param>
22 $cond_flavour.distance_method 96 <conditional name="cond_flavour">
23 --retree $cond_flavour.retree 97 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.">
24 --maxiterate $cond_flavour.iterations 98 <option value="mafft --auto">auto</option>
25 #end if 99 <option value="mafft-fftns" selected="true">fftns</option>
26 100 <option value="mafft-fftnsi">fftnsi</option>
27 ## specify threads to use 101 <option value="mafft-nwns">nwns</option>
28 --thread \${GALAXY_SLOTS:-1} 102 <option value="mafft-nwnsi">nwnsi</option>
29 103 <option value="mafft-einsi">einsi</option>
30 $datatype 104 <option value="mafft-ginsi">ginsi</option>
31 --ep $ep 105 <option value="mafft-linsi">linsi</option>
32 --op $op 106 <option value="mafft-qinsi">qinsi</option>
33 $adjustdirection 107 <option value="mafft-xinsi">xinsi</option>
34 108 <option value="custom">Custom Parameters</option>
35 #if $matrix_condition.matrix == "BLOSUM" 109 </param>
36 --bl ${matrix_condition.BLOSUM} 110 <when value="mafft-fftns"/>
37 #elif $matrix_condition.matrix == "PAM" 111 <when value="mafft --auto"/>
38 --jtt ${matrix_condition.PAM} 112 <when value="mafft-fftnsi"/>
39 #end if 113 <when value="mafft-nwns"/>
40 114 <when value="mafft-nwnsi"/>
41 $reorder 115 <when value="mafft-einsi"/>
42 $getTree 116 <when value="mafft-ginsi"/>
43 $outputFormat 117 <when value="mafft-linsi"/>
44 $inputSequences > $outputAlignment; 118 <when value="mafft-qinsi"/>
45 119 <when value="mafft-xinsi"/>
46 #if $getTree == "--treeout" 120 <when value="custom">
47 mv ${inputSequences}.tree $outputTree; 121 <conditional name="dist_flavour">
48 #end if 122 <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
49 ]]> 123 <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
50 </command> 124 <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
51 <inputs> 125 <option value="--localpair">Local alignment (Smith-Waterman)</option>
52 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> 126 <option value="--genafpair">Local, affine gap cost</option>
53 <param name="datatype" type="select" label="Data type"> 127 <option value="--fastapair">All pairwise alignments are computed with FASTA</option>
54 <option value="">Auto detection</option> 128 </param>
55 <option value="--nuc">Nucleic acids</option> 129 <when value="--6merpair">
56 <option value="--amino">Amino acids</option> 130 <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
131 <conditional name="usetree">
132 <param name="parttree" type="select" label="Use a fast tree-building method?" help="Recommended for a large number (> ~10,000) of sequences are input" >
133 <option value="--parttree" selected="true">Yes</option>
134 <option value="">No</option>
135 </param>
136 <when value="--parttree">
137 <param name="treedistance" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
138 <option value="--fastaparttree" selected="true">Distances based on FASTA</option>
139 <option value="--dpparttree">Distances based on DP. (Needleman-Wunsch)</option>
140 </param>
141 <param name="partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm" />
142 <param name="groupsize" type="integer" value="" min="0" max="1000" label="Do not make alignment larger than ... sequences" />
143 </when>
144 <when value=""/>
145 </conditional>
146 </when>
147 <when value="--globalpair">
148 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
149 </when>
150 <when value="--localpair">
151 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
152 <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
153 <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
154 <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
155 </when>
156 <when value="--genafpair">
157 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
158 <param name="lop" type="float" value="-2.0" label="Gap opening penalty at local pairwise alignment" help="-2.00 default value" />
159 <param name="lep" type="float" value="0.1" label="Offset value at local pairwise alignment" help="0.1 default value" />
160 <param name="lexp" type="float" value="-0.1" label="Gap extension penalty at local pairwise alignment." help="-0.1 default value" />
161 <param name="skipLOP" type="float" value="-6.00" label="Gap opening penalty to skip the alignment" help="-6.00 default value" />
162 <param name="skipEXP" type="float" value="0.00" label="Gap extension penalty to skip the alignment" help="0 default value" />
163 </when>
164 <when value="--fastapair">
165 <param name="weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments." help="Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected." />
166 </when>
167 </conditional>
168 <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
169 <param name="fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
170 <param name="score" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
171 </when>
172 </conditional>
173 <param name="ep" type="float" value="0.0" label="Gap extend penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
174 <param name="op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value" />
175 <conditional name="matrix_condition">
176 <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
177 <option value="">No matrix</option>
178 <option value="BLOSUM" selected="true">BLOSUM</option>
179 <option value="PAM">PAM</option>
180 <option value="custom">Custom</option>
181 </param>
182 <when value=""/>
183 <when value="BLOSUM">
184 <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
185 <option value="30">30</option>
186 <option value="45">45</option>
187 <option value="62" selected="true">62</option>
188 <option value="80">80</option>
57 </param> 189 </param>
58 <conditional name="cond_flavour"> 190 </when>
59 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section."> 191 <when value="PAM">
60 <option value="mafft --auto">auto</option> 192 <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the JTT PAM matrix" />
61 <option value="mafft-fftns" selected="true">fftns</option> 193 <param name="tm" type="integer" value="80" min="1" max="350" label="Coefficient of the transmembrane PAM matrix" />
62 <option value="mafft-fftnsi">fftnsi</option> 194 </when>
63 <option value="mafft-nwns">nwns</option> 195 <when value="custom">
64 <option value="mafft-nwnsi">nwnsi</option> 196 <param name="matrixfile" type="data" format="txt" label="User-defined AA scoring matrix" help="The format of matrixfile is the same to that of BLAST. Ignored when nucleotide sequences are input."/>
65 <option value="mafft-einsi">einsi</option> 197 <param name="fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition information into the scoring matrix?" />
66 <option value="mafft-ginsi">ginsi</option> 198 </when>
67 <option value="mafft-linsi">linsi</option> 199 </conditional>
68 <option value="mafft-qinsi">qinsi</option> 200 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
69 <option value="mafft-xinsi">xinsi</option> 201 <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
70 <option value="custom">Custom Parameters</option> 202 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
71 </param> 203 <option value="" selected="true">FASTA</option>
72 <when value="mafft-fftns"/> 204 <option value="--clustalout">ClustalW</option>
73 <when value="mafft --auto"/> 205 <option value="--phylipout">Phylip</option>
74 <when value="mafft-fftnsi"/> 206 </param>
75 <when value="mafft-nwns"/> 207 </inputs>
76 <when value="mafft-nwnsi"/> 208 <outputs>
77 <when value="mafft-einsi"/> 209 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
78 <when value="mafft-ginsi"/> 210 <change_format>
79 <when value="mafft-linsi"/> 211 <when input="outputFormat" value="--clustalout" format="clustal"/>
80 <when value="mafft-qinsi"/> 212 <when input="outputFormat" value="--phylipout" format="phylip"/>
81 <when value="mafft-xinsi"/> 213 </change_format>
82 <when value="custom"> 214 </data>
83 <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data"> 215 <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
84 <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option> 216 <filter>getTree == True</filter>
85 <option value="--globalpair">Global alignment (Needleman-Wunsch)</option> 217 </data>
86 <option value="--localpair">Local alignment (Smith-Waterman)</option> 218 </outputs>
87 <option value="--genafpair">Local, affine gap cost</option> 219 <tests>
88 </param> 220 <test expect_num_outputs="1" >
89 <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" /> 221 <param name="inputSequences" value="sample.fa"/>
90 <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" /> 222 <param name="flavourType" value="mafft-fftns"/>
91 </when> 223 <param name="outputFormat" value=""/>
92 </conditional> 224 <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>
93 <param name="ep" type="float" value="0.123" label="Gap extend penalty" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" /> 225 </test>
94 <param name="op" type="float" value="1.53" label="Gap opening penalty" help="1.53 default value" /> 226 <test expect_num_outputs="1" >
95 <param name="adjustdirection" type="select" display="radio" label="Direction of nucleotide sequences" help="Generate reverse complement sequences, as necessary, and align them together with the remaining sequences"> 227 <param name="inputSequences" value="sample.fa"/>
96 <option value="--adjustdirection">adjust direction</option> 228 <param name="flavourType" value="mafft-nwns"/>
97 <option value=" " selected="true">do not adjust direction</option> 229 <param name="outputFormat" value="--clustalout"/>
98 </param> 230 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/>
99 <conditional name="matrix_condition"> 231 </test>
100 <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" > 232 <test expect_num_outputs="1" >
101 <option value="">No matrix</option> 233 <param name="inputSequences" value="sample.fa"/>
102 <option value="BLOSUM">BLOSUM</option> 234 <param name="flavourType" value="custom"/>
103 <option value="PAM">PAM</option> 235 <param name="matrix_condition" value="BLOSUM"/>
104 </param> 236 <param name="BLOSUM" value="62"/>
105 <when value=""/> 237 <param name="distance_method" value="--fastapair"/>
106 <when value="BLOSUM"> 238 <param name="weighti" value="2.7"/>
107 <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix"> 239 <param name="iterations" value="1000"/>
108 <option value="30">30</option> 240 <param name="outputFormat" value="--clustalout"/>
109 <option value="45">45</option> 241 <output name="outputAlignment" ftype="clustal" file="mafft_custom_result.aln"/>
110 <option value="62" selected="true">62</option> 242 </test>
111 <option value="80">80</option> 243 </tests>
112 </param> 244 <help> <![CDATA[
113 </when> 245 **What it does**
114 <when value="PAM"> 246 MAFFT is a multiple sequence alignment program for unix-like operating systems.
115 <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the PAM matrix" /> 247 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
116 </when> 248 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
117 </conditional> 249 From the MAFFT man page, an overview of the different predefined flavours of the tool.
118 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" /> 250 **Accuracy-oriented methods:**
119 <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" /> 251 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
120 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW"> 252 - mafft --localpair --maxiterate 1000 input [> output]
121 <option value="" selected="true">FASTA</option> 253 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
122 <option value="--clustalout">ClustalW</option> 254 - mafft --globalpair --maxiterate 1000 input [> output]
123 <option value="--phylipout">Phylip</option> 255 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
124 </param> 256 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
125 </inputs> 257 **Speed-oriented methods:**
126 <outputs> 258 - FFT-NS-i (iterative refinement method; two cycles only):
127 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}"> 259 - mafft --retree 2 --maxiterate 2 input [> output]
128 <change_format> 260 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
129 <when input="outputFormat" value="--clustalout" format="clustal"/> 261 - mafft --retree 2 --maxiterate 1000 input [> output]
130 <when input="outputFormat" value="--phylipout" format="phylip"/> 262 - FFT-NS-2 (fast; progressive method):
131 </change_format> 263 - mafft --retree 2 --maxiterate 0 input [> output]
132 </data> 264 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
133 <data name="outputTree" format="txt" label="${tool.name} Guide Tree"> 265 - mafft --retree 1 --maxiterate 0 input [> output]
134 <filter>getTree == True</filter> 266 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
135 </data> 267 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
136 </outputs> 268 - NW-NS-2 (fast; progressive method without the FFT approximation):
137 <tests> 269 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
138 <test> 270 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
139 <param name="inputSequences" value="sample.fa"/> 271 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
140 <param name="flavourType" value="mafft-fftns"/> 272
141 <param name="outputFormat" value=""/> 273 **Options:**
142 <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/> 274 --auto
143 </test> 275 Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
144 <test> 276 --adjustdirection
145 <param name="inputSequences" value="sample.fa"/> 277 Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
146 <param name="flavourType" value="mafft-nwns"/> 278 --op
147 <param name="outputFormat" value="--clustalout"/> 279 Gap opening penalty, default: 1.53
148 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/> 280 --ep
149 </test> 281 Offset (works like gap extension penalty), default: 0.0
150 </tests> 282 --maxiterate
151 <help> 283 Maximum number of iterative refinement, default: 0
152 <![CDATA[ 284 --clustalout
153 **What it does** 285 Output: clustal format, default: fasta
154 286 --thread
155 MAFFT is a multiple sequence alignment program for unix-like operating systems. 287 Number of threads (if unsure, --thread -1)
156 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 288 --retree number
157 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. 289 Guide tree is built number times in the progressive stage.
158 290 Valid with 6mer distance. Default: 2
159 From the MAFFT man page, an overview of the different predefined flavours of the tool. 291 ]]>
160
161 **Accuracy-oriented methods:**
162
163 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
164
165 - mafft --localpair --maxiterate 1000 input [> output]
166
167 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
168
169 - mafft --globalpair --maxiterate 1000 input [> output]
170
171 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
172
173 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
174
175
176 **Speed-oriented methods:**
177
178 - FFT-NS-i (iterative refinement method; two cycles only):
179
180 - mafft --retree 2 --maxiterate 2 input [> output]
181
182 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
183
184 - mafft --retree 2 --maxiterate 1000 input [> output]
185
186 - FFT-NS-2 (fast; progressive method):
187
188 - mafft --retree 2 --maxiterate 0 input [> output]
189
190 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
191
192 - mafft --retree 1 --maxiterate 0 input [> output]
193
194 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
195
196 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
197
198 - NW-NS-2 (fast; progressive method without the FFT approximation):
199
200 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
201
202 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
203
204 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
205
206 **Options:**
207
208 --auto
209 Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
210 --adjustdirection
211 Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
212 --op
213 Gap opening penalty, default: 1.53
214 --ep
215 Offset (works like gap extension penalty), default: 0.0
216 --maxiterate
217 Maximum number of iterative refinement, default: 0
218 --clustalout
219 Output: clustal format, default: fasta
220 --thread
221 Number of threads (if unsure, --thread -1)
222 --retree number
223 Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
224 ]]>
225 </help> 292 </help>
226 <citations> 293 <expand macro="citations" />
227 <citation type="doi">10.1093/molbev/mst010</citation>
228 </citations>
229 </tool> 294 </tool>