raxml-ng.vital-it.ch
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Submitted URL: http://raxml-ng.vital-it.ch/
Effective URL: https://raxml-ng.vital-it.ch/
Submission: On December 11 via manual from IT — Scanned from CH
Effective URL: https://raxml-ng.vital-it.ch/
Submission: On December 11 via manual from IT — Scanned from CH
Form analysis
1 forms found in the DOMName: register_form —
<form data-v-167c63a6="" name="register_form" role="form" enctype="multipart/form-data">
<fieldset data-v-167c63a6="">
<legend data-v-167c63a6="" class="mylegend">Data</legend>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Paste your <b data-v-167c63a6="">sequence alignment</b></label></div>
<div data-v-167c63a6="" class="col"><textarea data-v-167c63a6="" id="txtSequenceAlign" rows="5" class="form-control"></textarea></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" role="alert" class="alert alert-primary"> Must be in <a data-v-167c63a6="" href="#/phylip" target="_blank">PHYLIP format, or FASTA format, or convertible by readseq</a></div>
</div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="fileUpload" class="float-right">or upload a file</label></div>
<div data-v-167c63a6="" class="col"><input data-v-167c63a6="" type="file" id="sequenceAlignment" accept=".fasta,.fa,.phylip"><!----></div>
<div data-v-167c63a6="" class="col"><!----></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Paste your <b data-v-167c63a6="">constraint tree</b></label></div>
<div data-v-167c63a6="" class="col"><textarea data-v-167c63a6="" id="txtSequenceAlign" rows="5" class="form-control"></textarea></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" role="alert" class="alert alert-primary"> This option allows you to specify an incomplete or comprehensive multifurcating constraint tree in NEWICK format. More help
<a data-v-167c63a6="" href="#/constraint" target="_blank">here</a>. </div>
</div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="fileUpload" class="float-right">or upload a file</label></div>
<div data-v-167c63a6="" class="col"><input data-v-167c63a6="" type="file" id="treeFile" accept=".newick"> <!----></div>
<div data-v-167c63a6="" class="col"><!----></div>
</div>
</fieldset>
<fieldset data-v-167c63a6="">
<legend data-v-167c63a6="" class="mylegend">Evolutionary model</legend>
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__12" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="partitionModelradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm"><input id="partitionModelradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="true"><span><span>Partitioned model</span></span></label><label class="btn btn-outline-primary btn-sm active"><input id="partitionModelradios__BV_radio_1_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="false"><span><span>Unpartitioned model</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" role="alert" class="alert alert-primary"> Model string is composed as described <a data-v-167c63a6="" href="https://github.com/amkozlov/raxml-ng/wiki/Input-data#single-model" target="_blank">here</a>. Individual model
modifiers are joined with “+” (plus sign). </div>
</div>
</div>
<div data-v-167c63a6="">
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Datatype</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__16" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="datatypesradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm active"><input id="datatypesradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="dna"><span><span>DNA</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="datatypesradios__BV_radio_1_opt_" type="radio" name="radiosBtnDefault"
autocomplete="off" class="" value="protein"><span><span>Protein/AA</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="datatypesradios__BV_radio_2_opt_" type="radio" name="radiosBtnDefault"
autocomplete="off" class="" value="binary"><span><span>Binary</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="datatypesradios__BV_radio_3_opt_" type="radio" name="radiosBtnDefault" autocomplete="off"
class="" value="multistate"><span><span>Multistate</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col"></div>
</div> <!---->
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" class="form-check-label float-right">Substitution matrix</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="text-center"><select data-v-167c63a6="" class="custom-select">
<option data-v-167c63a6="" value="JC"> JC </option>
<option data-v-167c63a6="" value="K80"> K80 </option>
<option data-v-167c63a6="" value="F81"> F81 </option>
<option data-v-167c63a6="" value="HKY"> HKY </option>
<option data-v-167c63a6="" value="TN93ef"> TN93ef </option>
<option data-v-167c63a6="" value="TN93"> TN93 </option>
<option data-v-167c63a6="" value="K81"> K81 </option>
<option data-v-167c63a6="" value="K81uf"> K81uf </option>
<option data-v-167c63a6="" value="TPM2"> TPM2 </option>
<option data-v-167c63a6="" value="TPM2uf"> TPM2uf </option>
<option data-v-167c63a6="" value="TPM3"> TPM3 </option>
<option data-v-167c63a6="" value="TPM3uf"> TPM3uf </option>
<option data-v-167c63a6="" value="TIM1"> TIM1 </option>
<option data-v-167c63a6="" value="TIM1uf"> TIM1uf </option>
<option data-v-167c63a6="" value="TIM2"> TIM2 </option>
<option data-v-167c63a6="" value="TIM2uf"> TIM2uf </option>
<option data-v-167c63a6="" value="TIM3"> TIM3 </option>
<option data-v-167c63a6="" value="TIM3uf"> TIM3uf </option>
<option data-v-167c63a6="" value="TVMef"> TVMef </option>
<option data-v-167c63a6="" value="TVM"> TVM </option>
<option data-v-167c63a6="" value="SYM"> SYM </option>
<option data-v-167c63a6="" value="GTR"> GTR </option>
</select></div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" class="form-check-label float-right">Stationary base frequencies</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__22" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="frequenciesradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm active"><input id="frequenciesradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="MLestimate"><span><span>ML estimate</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="frequenciesradios__BV_radio_1_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="empirical"><span><span>empirical</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="frequenciesradios__BV_radio_2_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="equal"><span><span>equal</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-check">
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="gammaModel" class="form-check-label float-right">Proportion of invariant sites</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="invariant" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="invariant" class="custom-control-label"></label></div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Among-site rate heterogeneity</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__28" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="heterogeneityradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm"><input id="heterogeneityradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="none"><span><span>None</span></span></label><label class="btn btn-outline-primary btn-sm active"><input id="heterogeneityradios__BV_radio_1_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="gamma"><span><span>GAMMA</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="heterogeneityradios__BV_radio_2_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="freeRate"><span><span>FreeRate</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Number of rate categories</label></div>
<div data-v-167c63a6="" class="col"><input data-v-167c63a6="" type="number" id="replyNumber" min="2" class="form-control"></div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right"> GAMMA category rates</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__33" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="gammaCategoriesRateradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm"><input id="gammaCategoriesRateradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="median"><span><span>median</span></span></label><label class="btn btn-outline-primary btn-sm active"><input id="gammaCategoriesRateradios__BV_radio_1_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="mean"><span><span>mean</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Ascertainment bias correction</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__37" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="biasCorrectionradios" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm active"><input id="biasCorrectionradios__BV_radio_0_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="none"><span><span>None</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="biasCorrectionradios__BV_radio_1_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="lewis"><span><span>Lewis</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="biasCorrectionradios__BV_radio_2_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="felsentein"><span><span>Felsentein</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="biasCorrectionradios__BV_radio_3_opt_" type="radio"
name="radiosBtnDefault" autocomplete="off" class="" value="stamatakis"><span><span>Stamatakis</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col"></div>
</div> <!---->
</div> <!---->
</fieldset>
<fieldset data-v-167c63a6="">
<legend data-v-167c63a6="" class="mylegend">Analysis</legend>
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="optimize" class="form-check-label float-right"><b data-v-167c63a6="" style="font-size: large;">ML tree search</b></label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="optimize" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label for="optimize"
class="custom-control-label"></label></div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="">
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="model" class="form-check-label float-right">Optimize</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="topology" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="topology" class="custom-control-label"> Topology </label></div>
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="branchLengths" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="branchLengths" class="custom-control-label"> Branch lengths </label></div>
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="model" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label for="model"
class="custom-control-label"> Model </label></div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div> <br data-v-167c63a6="">
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="MLtree" class="form-check-label float-right"><b data-v-167c63a6="" style="font-size: 15px; font-style: italic;">Starting trees</b></label></div>
<div data-v-167c63a6="" class="col"></div>
<div data-v-167c63a6="" class="col"></div>
</div><br data-v-167c63a6="">
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="parsimony" class="form-check-label float-right" style="font-size: 15px; font-style: italic;">Parsimony</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col-1">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="parsimony" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="parsimony" class="custom-control-label"></label></div>
</div>
<div data-v-167c63a6="" class="col-6"><label data-v-167c63a6="" for="ex1">Number of trees</label></div>
<div data-v-167c63a6="" class="col-5"><input data-v-167c63a6="" type="number" id="replyNumber" min="0" class="form-control"></div>
</div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="random" class="form-check-label float-right" style="font-size: 15px; font-style: italic;">Random</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col-1">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="random" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="random" class="custom-control-label"></label></div>
</div>
<div data-v-167c63a6="" class="col-6"><label data-v-167c63a6="" for="ex1">Number of trees</label></div>
<div data-v-167c63a6="" class="col-5"><input data-v-167c63a6="" type="number" id="replyNumber" min="0" class="form-control"></div>
</div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="userSpecifiedSequence" class="float-right" style="font-size: 15px; font-style: italic;">Paste your tree in newick format</label></div>
<div data-v-167c63a6="" class="col"><textarea data-v-167c63a6="" id="userSpecifiedSequence" rows="5" class="form-control"></textarea></div>
<div data-v-167c63a6="" class="col"></div>
</div>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="fileUpload" class="float-right" style="font-size: 15px; font-style: italic;">or upload a file</label></div>
<div data-v-167c63a6="" class="col"><input data-v-167c63a6="" type="file" id="startingTreeUserSpecified"><!----></div>
<div data-v-167c63a6="" class="col"><!----></div>
</div>
</div>
<div data-v-167c63a6="" class="row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="bootstrapping" class="form-check-label float-right"><b data-v-167c63a6="" style="font-size: large;">Bootstraping</b></label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="custom-control custom-checkbox custom-control-inline"><input id="bootstrapping" type="checkbox" autocomplete="off" true-value="true" false-value="false" class="custom-control-input" value="true"><label
for="bootstrapping" class="custom-control-label"></label></div>
</div>
<div data-v-167c63a6="" class="col"></div>
</div> <!---->
</fieldset>
<fieldset data-v-167c63a6="">
<legend data-v-167c63a6="" class="mylegend">Notification</legend>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Email</label></div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" class="col"><input data-v-167c63a6="" type="email" id="exampleFormControlInput1" placeholder="name@example.com" class="form-control "></div>
</div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" role="alert" class="alert alert-primary"> Enter your email if you want to be notified upon job completion </div>
</div>
</div>
</fieldset>
<fieldset data-v-167c63a6="">
<legend data-v-167c63a6="" class="mylegend">Anonymized Data Sharing</legend>
<div data-v-167c63a6="" class="form-group row">
<div data-v-167c63a6="" class="col"><label data-v-167c63a6="" for="txtSequenceAlign" class="float-right">Anonymized data sharing</label></div>
<div data-v-167c63a6="" class="col">
<fieldset data-v-167c63a6="" id="__BVID__50" role="group" class="b-form-group form-group"><!---->
<div role="group" class="">
<div data-v-167c63a6="" id="datasharing" role="radiogroup" tabindex="-1" class="btn-group-toggle btn-group"><label class="btn btn-outline-primary btn-sm active"><input id="datasharing__BV_radio_0_opt_" type="radio" name="radiosBtnDefault"
autocomplete="off" class="" value="no"><span><span>No</span></span></label><label class="btn btn-outline-primary btn-sm"><input id="datasharing__BV_radio_1_opt_" type="radio" name="radiosBtnDefault" autocomplete="off" class=""
value="yes"><span><span>Yes</span></span></label></div><!----><!----><!---->
</div>
</fieldset>
</div>
<div data-v-167c63a6="" class="col">
<div data-v-167c63a6="" role="alert" class="alert alert-primary"> More information about <a data-v-167c63a6="" href="#/terms" target="_blank">anonymized data sharing</a>. </div>
</div>
</div>
</fieldset> <button data-v-167c63a6="" type="submit" class="btn btn-primary btn-sm" style="margin-bottom: 10px;">Submit</button> <!---->
</form>
Text Content
Important note: RAxML Blackbox service on this server will be end of service in 31.01.2024. RAxML * Software * Mirror at CIPRES * Contact RAxML v1.0.0 RAXML BLACKBOX Data Paste your sequence alignment Must be in PHYLIP format, or FASTA format, or convertible by readseq or upload a file Paste your constraint tree This option allows you to specify an incomplete or comprehensive multifurcating constraint tree in NEWICK format. More help here. or upload a file Evolutionary model Partitioned modelUnpartitioned model Model string is composed as described here. Individual model modifiers are joined with “+” (plus sign). Datatype DNAProtein/AABinaryMultistate Substitution matrix JC K80 F81 HKY TN93ef TN93 K81 K81uf TPM2 TPM2uf TPM3 TPM3uf TIM1 TIM1uf TIM2 TIM2uf TIM3 TIM3uf TVMef TVM SYM GTR Stationary base frequencies ML estimateempiricalequal Proportion of invariant sites Among-site rate heterogeneity NoneGAMMAFreeRate Number of rate categories GAMMA category rates medianmean Ascertainment bias correction NoneLewisFelsenteinStamatakis Analysis ML tree search Optimize Topology Branch lengths Model Starting trees Parsimony Number of trees Random Number of trees Paste your tree in newick format or upload a file Bootstraping Notification Email Enter your email if you want to be notified upon job completion Anonymized Data Sharing Anonymized data sharing NoYes More information about anonymized data sharing. Submit When publishing results obtained via the web-server please cite: Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, and Alexandros Stamatakis (2019), RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, btz305 doi:10.1093/bioinformatics/btz305 © SIB Swiss Institute of Bioinformatics 2021 HITS Data Privacy