raxml-ng.vital-it.ch Open in urlscan Pro
192.42.198.13  Public Scan

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

Form analysis 1 forms found in the DOM

Name: 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
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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

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Anonymized Data Sharing
Anonymized data sharing
NoYes
More information about anonymized data sharing.
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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
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