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comparison qiime2/qiime_phylogeny_align-to-tree-mafft-iqtree.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?>
2 <tool id="qiime_phylogeny_align-to-tree-mafft-iqtree" name="qiime phylogeny align-to-tree-mafft-iqtree"
3 version="2020.8">
4 <description>Build a phylogenetic tree using iqtree and mafft alignment.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime phylogeny align-to-tree-mafft-iqtree
10
11 --i-sequences=$isequences
12
13 #if str($pnthreads) != 'None':
14 --p-n-threads=$pnthreads
15 #end if
16
17 --p-mask-max-gap-frequency=$pmaskmaxgapfrequency
18
19 --p-mask-min-conservation=$pmaskminconservation
20
21 #if str($psubstitutionmodel) != 'None':
22 --p-substitution-model=$psubstitutionmodel
23 #end if
24
25 #if $pfast:
26 --p-fast
27 #end if
28
29 #if str($palrt):
30 --p-alrt=$palrt
31 #end if
32 #if str($pseed):
33 --p-seed=$pseed
34 #end if
35 #if str($pstopiter):
36 --p-stop-iter=$pstopiter
37 #end if
38 #if str($pperturbnnistrength):
39 --p-perturb-nni-strength=$pperturbnnistrength
40 #end if
41 --o-alignment=oalignment
42
43 --o-masked-alignment=omaskedalignment
44
45 --o-tree=otree
46
47 --o-rooted-tree=orootedtree
48
49 #if str($examples) != 'None':
50 --examples=$examples
51 #end if
52
53 ;
54 cp orootedtree.qza $orootedtree
55
56 ]]></command>
57 <inputs>
58 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be used for creating a iqtree based rooted phylogenetic tree. [required]" name="isequences" optional="False" type="data" />
59 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
60 <option selected="True" value="None">Selection is Optional</option>
61 <option value="Int % Range(1">Int % Range(1</option>
62 <option value="None">None</option>
63 </param>
64 <param exclude_max="False" label="--p-mask-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. This value is used when masking the aligned sequences. [default: 1.0]" max="1" min="0" name="pmaskmaxgapfrequency" optional="True" type="float" value="1.0" />
65 <param exclude_max="False" label="--p-mask-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences. [default: 0.4]" max="1" min="0" name="pmaskminconservation" optional="True" type="float" value="0.4" />
66 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
67 <option selected="True" value="None">Selection is Optional</option>
68 <option value="JC">JC</option>
69 <option value="JC+I">JC+I</option>
70 <option value="JC+G">JC+G</option>
71 <option value="JC+I+G">JC+I+G</option>
72 <option value="JC+R2">JC+R2</option>
73 <option value="JC+R3">JC+R3</option>
74 <option value="JC+R4">JC+R4</option>
75 <option value="JC+R5">JC+R5</option>
76 <option value="JC+R6">JC+R6</option>
77 <option value="JC+R7">JC+R7</option>
78 <option value="JC+R8">JC+R8</option>
79 <option value="JC+R9">JC+R9</option>
80 <option value="JC+R10">JC+R10</option>
81 <option value="F81">F81</option>
82 <option value="F81+I">F81+I</option>
83 <option value="F81+G">F81+G</option>
84 <option value="F81+I+G">F81+I+G</option>
85 <option value="F81+R2">F81+R2</option>
86 <option value="F81+R3">F81+R3</option>
87 <option value="F81+R4">F81+R4</option>
88 <option value="F81+R5">F81+R5</option>
89 <option value="F81+R6">F81+R6</option>
90 <option value="F81+R7">F81+R7</option>
91 <option value="F81+R8">F81+R8</option>
92 <option value="F81+R9">F81+R9</option>
93 <option value="F81+R10">F81+R10</option>
94 <option value="K80">K80</option>
95 <option value="K80+I">K80+I</option>
96 <option value="K80+G">K80+G</option>
97 <option value="K80+I+G">K80+I+G</option>
98 <option value="K80+R2">K80+R2</option>
99 <option value="K80+R3">K80+R3</option>
100 <option value="K80+R4">K80+R4</option>
101 <option value="K80+R5">K80+R5</option>
102 <option value="K80+R6">K80+R6</option>
103 <option value="K80+R7">K80+R7</option>
104 <option value="K80+R8">K80+R8</option>
105 <option value="K80+R9">K80+R9</option>
106 <option value="K80+R10">K80+R10</option>
107 <option value="HKY">HKY</option>
108 <option value="HKY+I">HKY+I</option>
109 <option value="HKY+G">HKY+G</option>
110 <option value="HKY+I+G">HKY+I+G</option>
111 <option value="HKY+R2">HKY+R2</option>
112 <option value="HKY+R3">HKY+R3</option>
113 <option value="HKY+R4">HKY+R4</option>
114 <option value="HKY+R5">HKY+R5</option>
115 <option value="HKY+R6">HKY+R6</option>
116 <option value="HKY+R7">HKY+R7</option>
117 <option value="HKY+R8">HKY+R8</option>
118 <option value="HKY+R9">HKY+R9</option>
119 <option value="HKY+R10">HKY+R10</option>
120 <option value="TNe">TNe</option>
121 <option value="TNe+I">TNe+I</option>
122 <option value="TNe+G">TNe+G</option>
123 <option value="TNe+I+G">TNe+I+G</option>
124 <option value="TNe+R2">TNe+R2</option>
125 <option value="TNe+R3">TNe+R3</option>
126 <option value="TNe+R4">TNe+R4</option>
127 <option value="TNe+R5">TNe+R5</option>
128 <option value="TNe+R6">TNe+R6</option>
129 <option value="TNe+R7">TNe+R7</option>
130 <option value="TNe+R8">TNe+R8</option>
131 <option value="TNe+R9">TNe+R9</option>
132 <option value="TNe+R10">TNe+R10</option>
133 <option value="TN">TN</option>
134 <option value="TN+I">TN+I</option>
135 <option value="TN+G">TN+G</option>
136 <option value="TN+I+G">TN+I+G</option>
137 <option value="TN+R2">TN+R2</option>
138 <option value="TN+R3">TN+R3</option>
139 <option value="TN+R4">TN+R4</option>
140 <option value="TN+R5">TN+R5</option>
141 <option value="TN+R6">TN+R6</option>
142 <option value="TN+R7">TN+R7</option>
143 <option value="TN+R8">TN+R8</option>
144 <option value="TN+R9">TN+R9</option>
145 <option value="TN+R10">TN+R10</option>
146 <option value="K81">K81</option>
147 <option value="K81+I">K81+I</option>
148 <option value="K81+G">K81+G</option>
149 <option value="K81+I+G">K81+I+G</option>
150 <option value="K81+R2">K81+R2</option>
151 <option value="K81+R3">K81+R3</option>
152 <option value="K81+R4">K81+R4</option>
153 <option value="K81+R5">K81+R5</option>
154 <option value="K81+R6">K81+R6</option>
155 <option value="K81+R7">K81+R7</option>
156 <option value="K81+R8">K81+R8</option>
157 <option value="K81+R9">K81+R9</option>
158 <option value="K81+R10">K81+R10</option>
159 <option value="K81u">K81u</option>
160 <option value="K81u+I">K81u+I</option>
161 <option value="K81u+G">K81u+G</option>
162 <option value="K81u+I+G">K81u+I+G</option>
163 <option value="K81u+R2">K81u+R2</option>
164 <option value="K81u+R3">K81u+R3</option>
165 <option value="K81u+R4">K81u+R4</option>
166 <option value="K81u+R5">K81u+R5</option>
167 <option value="K81u+R6">K81u+R6</option>
168 <option value="K81u+R7">K81u+R7</option>
169 <option value="K81u+R8">K81u+R8</option>
170 <option value="K81u+R9">K81u+R9</option>
171 <option value="K81u+R10">K81u+R10</option>
172 <option value="TPM2">TPM2</option>
173 <option value="TPM2+I">TPM2+I</option>
174 <option value="TPM2+G">TPM2+G</option>
175 <option value="TPM2+I+G">TPM2+I+G</option>
176 <option value="TPM2+R2">TPM2+R2</option>
177 <option value="TPM2+R3">TPM2+R3</option>
178 <option value="TPM2+R4">TPM2+R4</option>
179 <option value="TPM2+R5">TPM2+R5</option>
180 <option value="TPM2+R6">TPM2+R6</option>
181 <option value="TPM2+R7">TPM2+R7</option>
182 <option value="TPM2+R8">TPM2+R8</option>
183 <option value="TPM2+R9">TPM2+R9</option>
184 <option value="TPM2+R10">TPM2+R10</option>
185 <option value="TPM2u">TPM2u</option>
186 <option value="TPM2u+I">TPM2u+I</option>
187 <option value="TPM2u+G">TPM2u+G</option>
188 <option value="TPM2u+I+G">TPM2u+I+G</option>
189 <option value="TPM2u+R2">TPM2u+R2</option>
190 <option value="TPM2u+R3">TPM2u+R3</option>
191 <option value="TPM2u+R4">TPM2u+R4</option>
192 <option value="TPM2u+R5">TPM2u+R5</option>
193 <option value="TPM2u+R6">TPM2u+R6</option>
194 <option value="TPM2u+R7">TPM2u+R7</option>
195 <option value="TPM2u+R8">TPM2u+R8</option>
196 <option value="TPM2u+R9">TPM2u+R9</option>
197 <option value="TPM2u+R10">TPM2u+R10</option>
198 <option value="TPM3">TPM3</option>
199 <option value="TPM3+I">TPM3+I</option>
200 <option value="TPM3+G">TPM3+G</option>
201 <option value="TPM3+I+G">TPM3+I+G</option>
202 <option value="TPM3+R2">TPM3+R2</option>
203 <option value="TPM3+R3">TPM3+R3</option>
204 <option value="TPM3+R4">TPM3+R4</option>
205 <option value="TPM3+R5">TPM3+R5</option>
206 <option value="TPM3+R6">TPM3+R6</option>
207 <option value="TPM3+R7">TPM3+R7</option>
208 <option value="TPM3+R8">TPM3+R8</option>
209 <option value="TPM3+R9">TPM3+R9</option>
210 <option value="TPM3+R10">TPM3+R10</option>
211 <option value="TPM3u">TPM3u</option>
212 <option value="TPM3u+I">TPM3u+I</option>
213 <option value="TPM3u+G">TPM3u+G</option>
214 <option value="TPM3u+I+G">TPM3u+I+G</option>
215 <option value="TPM3u+R2">TPM3u+R2</option>
216 <option value="TPM3u+R3">TPM3u+R3</option>
217 <option value="TPM3u+R4">TPM3u+R4</option>
218 <option value="TPM3u+R5">TPM3u+R5</option>
219 <option value="TPM3u+R6">TPM3u+R6</option>
220 <option value="TPM3u+R7">TPM3u+R7</option>
221 <option value="TPM3u+R8">TPM3u+R8</option>
222 <option value="TPM3u+R9">TPM3u+R9</option>
223 <option value="TPM3u+R10">TPM3u+R10</option>
224 <option value="TIMe">TIMe</option>
225 <option value="TIMe+I">TIMe+I</option>
226 <option value="TIMe+G">TIMe+G</option>
227 <option value="TIMe+I+G">TIMe+I+G</option>
228 <option value="TIMe+R2">TIMe+R2</option>
229 <option value="TIMe+R3">TIMe+R3</option>
230 <option value="TIMe+R4">TIMe+R4</option>
231 <option value="TIMe+R5">TIMe+R5</option>
232 <option value="TIMe+R6">TIMe+R6</option>
233 <option value="TIMe+R7">TIMe+R7</option>
234 <option value="TIMe+R8">TIMe+R8</option>
235 <option value="TIMe+R9">TIMe+R9</option>
236 <option value="TIMe+R10">TIMe+R10</option>
237 <option value="TIM">TIM</option>
238 <option value="TIM+I">TIM+I</option>
239 <option value="TIM+G">TIM+G</option>
240 <option value="TIM+I+G">TIM+I+G</option>
241 <option value="TIM+R2">TIM+R2</option>
242 <option value="TIM+R3">TIM+R3</option>
243 <option value="TIM+R4">TIM+R4</option>
244 <option value="TIM+R5">TIM+R5</option>
245 <option value="TIM+R6">TIM+R6</option>
246 <option value="TIM+R7">TIM+R7</option>
247 <option value="TIM+R8">TIM+R8</option>
248 <option value="TIM+R9">TIM+R9</option>
249 <option value="TIM+R10">TIM+R10</option>
250 <option value="TIM2e">TIM2e</option>
251 <option value="TIM2e+I">TIM2e+I</option>
252 <option value="TIM2e+G">TIM2e+G</option>
253 <option value="TIM2e+I+G">TIM2e+I+G</option>
254 <option value="TIM2e+R2">TIM2e+R2</option>
255 <option value="TIM2e+R3">TIM2e+R3</option>
256 <option value="TIM2e+R4">TIM2e+R4</option>
257 <option value="TIM2e+R5">TIM2e+R5</option>
258 <option value="TIM2e+R6">TIM2e+R6</option>
259 <option value="TIM2e+R7">TIM2e+R7</option>
260 <option value="TIM2e+R8">TIM2e+R8</option>
261 <option value="TIM2e+R9">TIM2e+R9</option>
262 <option value="TIM2e+R10">TIM2e+R10</option>
263 <option value="TIM2">TIM2</option>
264 <option value="TIM2+I">TIM2+I</option>
265 <option value="TIM2+G">TIM2+G</option>
266 <option value="TIM2+I+G">TIM2+I+G</option>
267 <option value="TIM2+R2">TIM2+R2</option>
268 <option value="TIM2+R3">TIM2+R3</option>
269 <option value="TIM2+R4">TIM2+R4</option>
270 <option value="TIM2+R5">TIM2+R5</option>
271 <option value="TIM2+R6">TIM2+R6</option>
272 <option value="TIM2+R7">TIM2+R7</option>
273 <option value="TIM2+R8">TIM2+R8</option>
274 <option value="TIM2+R9">TIM2+R9</option>
275 <option value="TIM2+R10">TIM2+R10</option>
276 <option value="TIM3e">TIM3e</option>
277 <option value="TIM3e+I">TIM3e+I</option>
278 <option value="TIM3e+G">TIM3e+G</option>
279 <option value="TIM3e+I+G">TIM3e+I+G</option>
280 <option value="TIM3e+R2">TIM3e+R2</option>
281 <option value="TIM3e+R3">TIM3e+R3</option>
282 <option value="TIM3e+R4">TIM3e+R4</option>
283 <option value="TIM3e+R5">TIM3e+R5</option>
284 <option value="TIM3e+R6">TIM3e+R6</option>
285 <option value="TIM3e+R7">TIM3e+R7</option>
286 <option value="TIM3e+R8">TIM3e+R8</option>
287 <option value="TIM3e+R9">TIM3e+R9</option>
288 <option value="TIM3e+R10">TIM3e+R10</option>
289 <option value="TIM3">TIM3</option>
290 <option value="TIM3+I">TIM3+I</option>
291 <option value="TIM3+G">TIM3+G</option>
292 <option value="TIM3+I+G">TIM3+I+G</option>
293 <option value="TIM3+R2">TIM3+R2</option>
294 <option value="TIM3+R3">TIM3+R3</option>
295 <option value="TIM3+R4">TIM3+R4</option>
296 <option value="TIM3+R5">TIM3+R5</option>
297 <option value="TIM3+R6">TIM3+R6</option>
298 <option value="TIM3+R7">TIM3+R7</option>
299 <option value="TIM3+R8">TIM3+R8</option>
300 <option value="TIM3+R9">TIM3+R9</option>
301 <option value="TIM3+R10">TIM3+R10</option>
302 <option value="TVMe">TVMe</option>
303 <option value="TVMe+I">TVMe+I</option>
304 <option value="TVMe+G">TVMe+G</option>
305 <option value="TVMe+I+G">TVMe+I+G</option>
306 <option value="TVMe+R2">TVMe+R2</option>
307 <option value="TVMe+R3">TVMe+R3</option>
308 <option value="TVMe+R4">TVMe+R4</option>
309 <option value="TVMe+R5">TVMe+R5</option>
310 <option value="TVMe+R6">TVMe+R6</option>
311 <option value="TVMe+R7">TVMe+R7</option>
312 <option value="TVMe+R8">TVMe+R8</option>
313 <option value="TVMe+R9">TVMe+R9</option>
314 <option value="TVMe+R10">TVMe+R10</option>
315 <option value="TVM">TVM</option>
316 <option value="TVM+I">TVM+I</option>
317 <option value="TVM+G">TVM+G</option>
318 <option value="TVM+I+G">TVM+I+G</option>
319 <option value="TVM+R2">TVM+R2</option>
320 <option value="TVM+R3">TVM+R3</option>
321 <option value="TVM+R4">TVM+R4</option>
322 <option value="TVM+R5">TVM+R5</option>
323 <option value="TVM+R6">TVM+R6</option>
324 <option value="TVM+R7">TVM+R7</option>
325 <option value="TVM+R8">TVM+R8</option>
326 <option value="TVM+R9">TVM+R9</option>
327 <option value="TVM+R10">TVM+R10</option>
328 <option value="SYM">SYM</option>
329 <option value="SYM+I">SYM+I</option>
330 <option value="SYM+G">SYM+G</option>
331 <option value="SYM+I+G">SYM+I+G</option>
332 <option value="SYM+R2">SYM+R2</option>
333 <option value="SYM+R3">SYM+R3</option>
334 <option value="SYM+R4">SYM+R4</option>
335 <option value="SYM+R5">SYM+R5</option>
336 <option value="SYM+R6">SYM+R6</option>
337 <option value="SYM+R7">SYM+R7</option>
338 <option value="SYM+R8">SYM+R8</option>
339 <option value="SYM+R9">SYM+R9</option>
340 <option value="SYM+R10">SYM+R10</option>
341 <option value="GTR">GTR</option>
342 <option value="GTR+I">GTR+I</option>
343 <option value="GTR+G">GTR+G</option>
344 <option value="GTR+I+G">GTR+I+G</option>
345 <option value="GTR+R2">GTR+R2</option>
346 <option value="GTR+R3">GTR+R3</option>
347 <option value="GTR+R4">GTR+R4</option>
348 <option value="GTR+R5">GTR+R5</option>
349 <option value="GTR+R6">GTR+R6</option>
350 <option value="GTR+R7">GTR+R7</option>
351 <option value="GTR+R8">GTR+R8</option>
352 <option value="GTR+R9">GTR+R9</option>
353 <option value="GTR+R10">GTR+R10</option>
354 <option value="MFP">MFP</option>
355 <option value="TEST">TEST</option>
356 </param>
357 <param label="--p-fast: --p-fast: / --p-no-fast Fast search to resemble FastTree. [default: False]" name="pfast" selected="False" type="boolean" />
358 <param label="--p-alrt: INTEGER Single branch test method. Number of bootstrap Range(1000, None) replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. [optional]" name="palrt" optional="False" type="text" />
359 <param label="--p-seed: INTEGER Random number seed for the iqtree parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
360 <param label="--p-stop-iter: INTEGER Number of unsuccessful iterations to stop. If not Range(1, None) set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pstopiter" optional="False" type="text" />
361 <param label="--p-perturb-nni-strength: NUMBER Range(0.01, 1.0) Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pperturbnnistrength" optional="False" type="text" />
362 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
363
364 </inputs>
365
366 <outputs>
367 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
368 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
369 <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
370 <data format="qza" label="${tool.name} on ${on_string}: rootedtree.qza" name="orootedtree" />
371
372 </outputs>
373
374 <help><![CDATA[
375 Build a phylogenetic tree using iqtree and mafft alignment.
376 ###############################################################
377
378 This pipeline will start by creating a sequence alignment using MAFFT,
379 after which any alignment columns that are phylogenetically uninformative
380 or ambiguously aligned will be removed (masked). The resulting masked
381 alignment will be used to infer a phylogenetic tree using IQ-TREE. By
382 default the best fit substitution model will be determined by ModelFinder
383 prior to phylogenetic inference. The resulting tree will be subsequently
384 rooted at its midpoint. Output files from each step of the pipeline will be
385 saved. This includes both the unmasked and masked MAFFT alignment from
386 q2-alignment methods, and both the rooted and unrooted phylogenies from
387 q2-phylogeny methods.
388
389 Parameters
390 ----------
391 sequences : FeatureData[Sequence]
392 The sequences to be used for creating a iqtree based rooted
393 phylogenetic tree.
394 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
395 The number of threads. (Use 0 to automatically use all available cores
396 This value is used when aligning the sequences and creating the tree
397 with iqtree.
398 mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
399 The maximum relative frequency of gap characters in a column for the
400 column to be retained. This relative frequency must be a number between
401 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
402 gap characters, and 1.0 retains all columns regardless of gap
403 character frequency. This value is used when masking the aligned
404 sequences.
405 mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
406 The minimum relative frequency of at least one non-gap character in a
407 column for that column to be retained. This relative frequency must be
408 a number between 0.0 and 1.0 (inclusive). For example, if a value of
409 0.4 is provided, a column will only be retained if it contains at
410 least one character that is present in at least 40% of the sequences.
411 This value is used when masking the aligned sequences.
412 substitution_model : Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
413 Model of Nucleotide Substitution. If not provided, IQ-TREE will
414 determine the best fit substitution model automatically.
415 fast : Bool, optional
416 Fast search to resemble FastTree.
417 alrt : Int % Range(1000, None), optional
418 Single branch test method. Number of bootstrap replicates to perform an
419 SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
420 replicates is recomended.
421 seed : Int, optional
422 Random number seed for the iqtree parsimony starting tree. This allows
423 you to reproduce tree results. If not supplied then one will be
424 randomly chosen.
425 stop_iter : Int % Range(1, None), optional
426 Number of unsuccessful iterations to stop. If not set, program defaults
427 will be used. See IQ-TREE manual for details.
428 perturb_nni_strength : Float % Range(0.01, 1.0), optional
429 Perturbation strength for randomized NNI. If not set, program defaults
430 will be used. See IQ-TREE manual for details.
431
432 Returns
433 -------
434 alignment : FeatureData[AlignedSequence]
435 The aligned sequences.
436 masked_alignment : FeatureData[AlignedSequence]
437 The masked alignment.
438 tree : Phylogeny[Unrooted]
439 The unrooted phylogenetic tree.
440 rooted_tree : Phylogeny[Rooted]
441 The rooted phylogenetic tree.
442 ]]></help>
443 <macros>
444 <import>qiime_citation.xml</import>
445 </macros>
446 <expand macro="qiime_citation"/>
447 </tool>