Mercurial > repos > abims-sbr > concatphyl
diff ConcatPhyl.xml @ 0:6d930f037fea draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
| author | abims-sbr |
|---|---|
| date | Thu, 13 Apr 2017 05:49:32 -0400 |
| parents | |
| children | 1f8d039bd241 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ConcatPhyl.xml Thu Apr 13 05:49:32 2017 -0400 @@ -0,0 +1,589 @@ +<tool name="ConcatPhyl" id="concatphyl" version="1.0"> + + <description> + Concatenation and phylogeny + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <expand macro="python_required" /> + <!-- <requirement type="package" version="1.3.1">samtools</requirement> --> + <requirement type="package" version="8.2.9">raxml</requirement> + </requirements> + + <command><![CDATA[ + python $__tool_directory__/scripts/S01_concatenate.py ${zip} + + #if $format.format_run == "nucleic" : + nucleic $format.zip_nuc + #elif $format.format_run == "proteic" : + proteic $format.zip_aa + #end if + > ${output}; + + raxmlHPC + #if $format.format_run == "nucleic" : + -n "galaxy_run" + ##-q "./05_partitions_gene_NUC" + -s "./03_Concatenation_nuc.phy" + ## (-m) + -m $format.base_model + #elif $format.format_run == "proteic" : + -n "galaxy_run" + ##-q "./06_partitions_gene_AA" + -s "./02_Concatenation_aa.phy" + ## (-m) + -m $format.base_model$format.aa_search_matrix + #end if + + ## --- Optional parameters --- + + ##if $raxml_options.options == "yes" : + + ## (-p) + #if $random_seed: + -p $random_seed + #else + -p 1234567890 + #end if + + ## (-N/#) + #if $number_of_runs: + -N $number_of_runs + #end if + #if $number_of_runs_bootstop: + -# $number_of_runs_bootstop + #end if + + ## (-f) + #if $search_algorithm: + -f $search_algorithm + #end if + + ## (-x) + #if $rapid_bootstrap_random_seed: + -x $rapid_bootstrap_random_seed + #end if + ##else : + + ##-N 100 -f a -x 12345 + + ##end if + >> ${output}; + ]]> + </command> + + <inputs> + + <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" /> + <conditional name="format"> + <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? "> + <option value="nucleic">Nucleic format</option> + <option value="proteic">Proteic format</option> + </param> + + <when value="nucleic"> + <param name="zip_nuc" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="It must contain the aligned files without indels in NUCLEIC format" /> + <!-- ## Nucleotide substitution models --> + <param name="base_model" type="select" label="Substitution Model"> + <option value="GTRCAT">GTRCAT</option> + <option value="GTRCATI">GTRCATI</option> + <option value="GTRGAMMA" selected="true">GTRGAMMA</option> + <option value="GTRGAMMAI">GTRGAMMAI</option> + </param> + </when> + + <when value="proteic"> + <param name="zip_aa" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="It must contain the aligned files without indels in PROTEIC format" /> + <!-- ## Aminoacid substitution models --> + <!--<param name="aa_model_empirical_base_frequencies" type="boolean" checked="no" truevalue="F" falsevalue="X" display="checkboxes" label="Use empirical base frequencies in AA models." /> --> + <param name="base_model" type="select" label="Substitution Model (-m)"> + <option value="PROTCAT" selected="true">PROTCAT</option> + <option value="PROTCATI">PROTCATI</option> + <option value="PROTGAMMA">PROTGAMMA</option> + <option value="PROTGAMMAI">PROTGAMMAI</option> + </param> + <param name="aa_search_matrix" type="select" label="Matrix"> + <option value="DAYHOFF" selected="true">DAYHOFF</option> + <option value="JTT">JTT</option> + <option value="WAG">WAG</option> + <option value="BLOSUM62">BLOSUM62</option> + </param> + </when> + </conditional> + +<!-- <conditional name="raxml_options"> --> + +<!-- +<param name="options" type="select" label="Raxml advanced options"> + <option value="yes">Yes</option> + <option value="no" select="true">No</option> +</param> + +--> + +<!-- <when value="yes"> --> + + <param name="random_seed" type="integer" value="1234567890" size="12" label="Random seed used for the parsimony inferences" /> + + <!-- ## (-N/#) --> + <param name="number_of_runs" type="integer" size="8" value="100" + label="Number of runs" help="Specify the number of + alternative runs (-N|#) on distinct starting trees In combination + with the '-b' option will invoke a multiple boostrap analysis. + You can add the bootstopping criteria by choosing the autoMR, + autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of + providing a number here. Bootstopping will only work in + combination with '-x' or '-b'." + optional="True" /> + <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True"> + <option value="" selected="yes"></option> + <option value="autoMR">autoMR</option> + <option value="autoMRE">autoMRE</option> + <option value="autoMRE_IGN">autoMRE_IGN</option> + <option value="autoFC">autoFC</option> + </param> + + <!-- ## (-f) --> + <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True"> + <option value="a">Rapid bootstrap and best ML tree search (a)</option> + <option value="A">Compute marginal ancestral states (A)</option> + <option value="b">Draw bipartition information (b)</option> + <option value="c">Check if the alignment can be read (c)</option> + <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option> + <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option> + <option value="g">Compute per-site log likelihoods for -z trees (g)</option> + <option value="h">Compute log likelihood test for -t / -z trees (h)</option> + <option value="j">Generate bootstrapped alignment files (j)</option> + <option value="J">Compute SH-like support values for the -t tree (J)</option> + <option value="m">Compare bipartitions between -t and -z trees (m)</option> + <option value="n">Compute log likelihood score for -z trees (n)</option> + <option value="o">Use old slower search algorithm (o)</option> + <option value="p">Stepwise MP addition of new sequences (p)</option> + <option value="q">Fast quartet calculator (q)</option> + <option value="r">Compute pairwise RF distances in -z trees (r)</option> + <option value="s">Split a multi-gene alignment (s)</option> + <option value="S">Compute site-specific placement bias (S)</option> + <option value="t">Randomized tree searches on a fixed starting tree (t)</option> + <option value="T">Final optimization of a ML tree from a bootstrap (T)</option> + <option value="u">Morphological weight calibration using ML on a -t tree (u)</option> + <option value="v">Classify environmental sequences (v)</option> + <option value="w">Compute ELW-test on -z trees (w)</option> + <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> + <option value="y">Classify environmental sequences into a reference tree (y)</option> + </param> + + <!-- ## (-q) --> + <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." /> + + <!-- ## (-x) --> + <param name="rapid_bootstrap_random_seed" type="integer" value='1234567890' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." /> +<!-- </when> --> + + +<!-- </conditional> --> + + <param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? "> + <option value="nothing">No output</option> + <option value="fasta">Fasta format</option> + <option value="phylip">Phylip format</option> + <option value="nexus">Nexus format</option> + </param> + <!-- -m GTRGAMMA -N 100 -f a -x 12345 --> + + <param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " /> + <param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " /> + <param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/> + + </inputs> + + <outputs> + <data name="output" format="txt" label="Phylogeny"/> + + <data name="out_fasta_aa" format="fasta" label="Phylogeny_concatenation_fasta_aa" from_work_dir="02_Concatenation_aa.fas"> + <filter>format['format_run'] == "proteic" and out == "fasta"</filter> + </data> + + <data name="out_phylip_aa" format="phylip" label="Phylogeny_concatenation_phylip_aa" from_work_dir="02_Concatenation_aa.phy"> + <filter>format['format_run'] == "proteic" and out == "phylip"</filter> + </data> + + <data name="out_nexus_aa" format="nexus" label="Phylogeny_concatenation_nexus_aa" from_work_dir="02_Concatenation_aa.nex"> + <filter>format['format_run'] == "proteic" and out == "nexus"</filter> + </data> + + <data name="out_fasta_nuc" format="fasta" label="Phylogeny_concatenation_fasta_nuc" from_work_dir="03_Concatenation_nuc.fas"> + <filter>format['format_run'] == "nucleic" and out == "fasta"</filter> + </data> + + <data name="out_phylip_nuc" format="phylip" label="Phylogeny_concatenation_phylip_nuc" from_work_dir="03_Concatenation_nuc.phy"> + <filter>format['format_run'] == "nucleic" and out == "phylip"</filter> + </data> + + <data name="out_nexus_nuc" format="nexus" label="Phylogeny_concatenation_nexus_nuc" from_work_dir="03_Concatenation_nuc.nex"> + <filter>format['format_run'] == "nucleic" and out == "nexus"</filter> + </data> + + <data name="out_raxml1" format="txt" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run"> + <filter>raxml1 == True</filter> + </data> + + <data name="out_raxml3" format="txt" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run"> + <filter>raxml3 == True</filter> + </data> + + <data name="out_raxml4" format="txt" label="Phylogeny_RAxML_BootStrap" from_work_dir="RAxML_bootstrap.galaxy_run"> + <filter>raxml4 == True</filter> + </data> + </outputs> + + <tests> + <test> + <param name="zip" ftype="zip" value="from_filter_oase.zip" /> + <conditional name="format"> + <param name="format_run" value="nucleic" /> + <param name="zip_nuc" ftype="zip" value="test_05_output_CDS_Search_input_ConcatPhyl.zip" /> + <param name="base_model" value="GTRGAMMA" /> + </conditional> + <param name="random_seed" value="1234567890" /> + <param name="number_of_runs" value="100" /> + <param name="number_of_runs_bootstop" value="" /> + <param name="search_algorithm" value="d" /> + <!-- <param name="multiple_model" value="" /> --> + <param name="rapid_bootstrap_random_seed" value="123456789" /> + <param name="out" value="nothing" /> + <param name="raxml1" value="True" /> + <param name="raxml3" value="True" /> + <param name="raxml4" value="True" /> + <output name="out_raxml4"> + <assert_contents> + <has_text text="(Ap,(((Pf,Ph),Pg),((Pu,Te),(Am,Th))),Ac);"/> + <has_text text="(Ap,(Ph,(Pg,((Pf,(Pu,Te)),(Am,Th)))),Ac);"/> + <has_text text="(Ap,(((Pu,Te),(Am,Th)),((Pf,Ph),Pg)),Ac);"/> + </assert_contents> + </output> + + </test> + </tests> + + <help> + +============ +What it does +============ + +| This tool takes a zip file containing nucleic fasta sequence files and searches different homologous genes from pairwise comparisons. +| +| +| The run RAxML was written by **Alexandros Stamatakis**. +| The script was written by **Eric Fontanillas**. +| The wrapper was written by **Julie Baffard**. + +-------- + +========== +Parameters +========== + +| The choice of the format sequences is possible : **proteic** or **nucleic** +| + +The choice of parameters for the RAxML run is possible : + +**-m** : + | is the option for the choice of the substitution model. + | By default it's GTRGAMMA. + | + +**-N** : + | is the option for the choice of the number of run + | by default it's 100 + | + +**rapid bootstrapping** : + | is the option to have, in addition to the best tree search, the rapid bootstrapping + | this translates by : -x 12345 -f a + | by default, this option is choosen + | + +-------- + +====== +Inputs +====== + +option **Select a zip file containing the input files** : + +| the input zip file must have the extension .ort.zip +| At the beginning, when you upload your input, you have to change the extension .zip to .ort.zip + + +-------- + +======= +Outputs +======= + +This tool, produces the following files : + +**Phylogeny** : + | is the general output. It gives the information about the concatenation (statistics) and the RAxML run. + | + +**Phylogeny_concatenation_fasta_aa** : + | is the output which contains the sequences concatenated in fasta format when you choose the option proteic + | + +**Phylogeny_concatenation_phylip_aa** : + | is the output which contains the sequences concatenated in phylip format when you choose the option proteic + | + +**Phylogeny_concatenation_nexus_aa** : + | is the output which contains the sequences concatenated in nexus format when you choose the option proteic + | + +**Phylogeny_concatenation_fasta_nuc** : + | is the output which contains the sequences concatenated in fasta format when you choose the option nucleic + | + +**Phylogeny_concatenation_phylip_nuc** : + | is the output which contains the sequences concatenated in phylip format when you choose the option nucleic + | it's this output which is used for the RAxML run + | + +**Phylogeny_concatenation_nexus_nuc** : + | is the output which contains the sequences concatenated in nexus format when you choose the option nucleic + | + +**Phylogeny_RAxML_BestTree** : + | is the output of RAxML run which contains the Best Tree found + | + +**Phylogeny_RAxML_BiPartitionBranchLabel** : + | is the output of RAxML run which contains the Best Tree found with supported values as branch labels + | + +**Phylogeny_RAxML_BiPartition** : + | is the output of RAxML run which contains the Best Tree found with supported values + | + +**Phylogeny_RAxML_BootStrap** : + | is the output of RAxML run which contains all the boostrapped trees + | the number of boostraped trees depending of the option -N (number of run) + | + +-------- + +=============== +Working Example +=============== + +--------------------------- +The input files and options +--------------------------- + +**Input files** + | 6 files with 200 nucleic sequences each + | a zip file containing 2 locus aligned without indel (in nucleic format) + | +**Parameters** + | option : nucleic + | no option for the RAxML run, so by default it's : -m GTRGAMMA -N 100 -f a -x 12345 + | + +---------------- +The output files +---------------- + +**Phylogeny** : + +| ******************** CONCATENATION ******************** +| +| Process nucleotides concatenation: +| Number of taxa aligned = 6 +| Number of loci concatenated = 2 +| +| Total length of the concatenated sequences [All codon positions] = 504 +| Total length of the concatenated sequences [Codon positions 1 and 2] = 336 +| Total length of the concatenated sequences [Codon position 3] = 168 +| +| +| +| ******************** RAxML RUN ******************** +| + +the informations of the RAxML run + +| + +**Phylogeny_concatenation_fasta_nuc** : + +| >Ps + +cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca +gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt +taccctctttgtctatcttgcataatccagcccat + +| Ac + +cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc +ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc--------------------------------------------------------- +------------------------ + +| >Pp +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +| ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat + +| >Ap + +cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc +ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt +ccgggccttgccttccttgtctatcttgcaaagaccagcccat + +| >Pf + +ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga +cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac +cttccttgctttcccttctttgtcaatcttgcataatccggcccat + +| >Pg + +cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg +tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc +cttgccttccttgtctatcttacacaagccagcccat + +.. class:: infomark + +| If you choose the option proteic : you obtain a file with proteic sequences +| +| + + +**Phylogeny_concatenation_phylip_nuc** : + +| 6 504 +| Ps + +cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca +gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt +taccctctttgtctatcttgcataatccagcccat + +| Ac + +cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc +ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc--------------------------------------------------------- +------------------------ + +| Pp +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +| ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat +| +| Ap + +cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc +ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt +ccgggccttgccttccttgtctatcttgcaaagaccagcccat + +Pf +ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga +cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac +cttccttgctttcccttctttgtcaatcttgcataatccggcccat + +Pg +cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg +tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc +cttgccttccttgtctatcttacacaagccagcccat + +.. class:: infomark + +| If you choose the option proteic : you obtain a file with proteic sequences +| +| + +**Phylogeny_concatenation_nexus_nuc** : + +#NEXUS + +| Begin data; +| Dimensions ntax=6 nchar=504; +| Format datatype=dna gap=-; + +Matrix + +Ps cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtct +ccagaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttcct +tgctttaccctctttgtctatcttgcataatccagcccat + +Ac cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttc +ggcggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc--------------------------------------------------- +------------------------------ + +Pp ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +-----------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat + +Ap cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttc +ggcggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaa +ccttccgggccttgccttccttgtctatcttgcaaagaccagcccat + +Pf ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctcc +gacgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgaca +accttccttgctttcccttctttgtcaatcttgcataatccggcccat + +Pg cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccg +acgtctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttc +ttgccttgccttccttgtctatcttacacaagccagcccat + +| ; +| End; +| + +.. class:: infomark + +| If you choose the option proteic : you obtain a file with proteic sequences +| +| + +**Phylogeny_RAxML_BestTree** : + +| ((Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217, +| ((Pp:0.23405795780876006984,Pg:0.02012322210145659623):0.14429203507314311561,Pf:0.09977363663005259231):0.04320803212100913365,Ps:0.08351583721596630983):0.0; +| +| + + +**Phylogeny_RAxML_BiPartitionBranchLabel** : + +| (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983, +| (Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217[89]):0.04320803212100913365[42]):0.14429203507314311561[70],Pp:0.23405795780876006984); +| +| + + +**Phylogeny_RAxML_BiPartition** : + +(Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983, +(Ac:0.02889451913999640381,Ap:0.01674414484251282934)89:0.17730049470177636217)42:0.04320803212100913365)70:0.14429203507314311561,Pp:0.23405795780876006984); + +| +| + +**Phylogeny_RAxML_BootStrap** : + +| ((Ap,Ac),((Pp,Pg),Pf),Ps); +| ((Ap,Ac),((Pp,Pg),Pf),Ps); +| (Pf,((Ap,Ac),(Pp,Pg)),Ps); +| ((Ap,Ac),((Pp,Pg),Pf),Ps); +| ((Ap,Ac),((Pp,Pg),Pf),Ps); +| ((Ap,Ac),((Pp,Pg),Pf),Ps); +| ((Pp,Pg),(Pf,(Ap,Ac)),Ps); + +... + + </help> + + <expand macro="citations" /> + +</tool>