Mercurial > repos > abims-sbr > concatphyl
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
author | abims-sbr |
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date | Thu, 13 Apr 2017 05:49:32 -0400 |
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children | 1f8d039bd241 |
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<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>