<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">4.1.4</token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btv351</citation>
        </citations>
    </xml>

    <xml name="augustus_species">
        <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->
        <option value="human">Homo sapiens</option>
        <option value="fly">Drosophila melanogaster</option>
        <option value="arabidopsis">Arabidopsis thaliana</option>
        <option value="brugia ">Brugia malayi</option>
        <option value="aedes">Aedes aegypti</option>
        <option value="tribolium2012">Tribolium castaneum</option>
        <option value="schistosoma">Schistosoma mansoni</option>
        <option value="tetrahymena">Tetrahymena thermophila</option>
        <option value="galdieria">Galdieria sulphuraria</option>
        <option value="maize">Zea mays</option>
        <option value="toxoplasma">Toxoplasma gondii</option>
        <option value="caenorhabditis ">Caenorhabditis elegans</option>
        <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>
        <option value="aspergillus_nidulans ">Aspergillus nidulans</option>
        <option value="aspergillus_oryzae ">Aspergillus oryzae</option>
        <option value="aspergillus_terreus">Aspergillus terreus</option>
        <option value="botrytis_cinerea ">Botrytis cinerea</option>
        <option value="candida_albicans ">Candida albicans</option>
        <option value="candida_guilliermondii ">Candida guilliermondii</option>
        <option value="candida_tropicalis ">Candida tropicalis</option>
        <option value="chaetomium_globosum">Chaetomium globosum</option>
        <option value="coccidioides_immitis">Coccidioides immitis</option>
        <option value="coprinus">Coprinus cinereus</option>
        <option value="coprinus_cinereus">Coprinus cinereus</option>
        <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>
        <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>
        <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>
        <option value="cryptococcus">Cryptococcus neoformans</option>
        <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>
        <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>
        <option value="eremothecium_gossypii">Eremothecium gossypii</option>
        <option value="fusarium_graminearum ">Fusarium graminearum</option>
        <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>
        <option value="histoplasma">Histoplasma capsulatum</option>
        <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>
        <option value="laccaria_bicolor ">Laccaria bicolor</option>
        <option value="lamprey">Petromyzon marinus</option>
        <option value="leishmania_tarentolae">Leishmania tarentolae</option>
        <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>
        <option value="magnaporthe_grisea ">Magnaporthe grisea</option>
        <option value="neurospora_crassa">Neurospora crassa</option>
        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
        <option value="pichia_stipitis">Pichia stipitis</option>
        <option value="rhizopus_oryzae">Rhizopus oryzae</option>
        <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>
        <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>
        <option value="saccharomyces">Saccharomyces cerevisiae</option>
        <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
        <option value="trichinella">Trichinella spiralis</option>
        <option value="ustilago_maydis">Ustilago maydis</option>
        <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
        <option value="nasonia">Nasonia vitripennis</option>
        <option value="tomato">Solanum lycopersicum</option>
        <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
        <option value="amphimedon">Amphimedon queenslandica</option>
        <option value="pneumocystis">Pneumocystis jirovecii</option>
        <option value="chicken">Gallus gallus domesticus (chicken)</option>
        <option value="cacao">Theobroma cacao (cacao)</option>
        <option value="heliconius_melpomene1">Heliconius melpomene</option>
        <option value="xenoturbella">Xenoturbella</option>
        <option value="E_coli_K12">E coli K12</option>
        <option value="c_elegans_trsk">c elegans trsk</option>
        <option value="camponotus_floridanus">Camponotus floridanus</option>
        <option value="coyote_tobacco">Coyote tobacco</option>
        <option value="s_aureus">Staphylococcus aureus</option>
        <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option>
        <option value="wheat">wheat</option>
        <option value="zebrafish">Danio rerio</option>
        <option value="anidulans">Aspergillus nidulans</option>
        <option value="bombus_impatiens1">Bombus impatiens1</option>
        <option value="bombus_terrestris2">Bombus terrestris2</option>
        <option value="botrytis_cinerea">Botrytis cinerea</option>
        <option value="brugia_malayi">Brugia malayi</option>
        <option value="conidiobolus_coronatus">Conidiobolus coronatus</option>
        <option value="cryptococcus_neoformans">Cryptococcus neoformans</option>
        <option value="culex_pipiens">Culex pipiens</option>
        <option value="elephant_shark">Callorhinchus milii</option>
        <option value="honeybee1">Apis mellifera</option>
        <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>
        <option value="pea_aphid">Acyrthosiphon pisum</option>
        <option value="rhodnius_prolixus">Rhodnius prolixus</option>
        <option value="ustilago_maydis">Ustilago maydis</option>
        <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option>
        <option value="verticillium_longisporum1">Verticillium longisporum1</option>
        <option value="Xipophorus_maculatus">Xipophorus_maculatus</option>
        <option value="adorsata">adorsata</option>
        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
        <option value="maker2_athal1">maker2_athal1</option>
        <option value="maker2_c_elegans1">maker2_c_elegans1</option>
        <option value="maker2_dmel1">maker2_dmel1</option>
        <option value="maker2_spomb1">maker2_spomb1</option>
        <option value="parasteatoda">parasteatoda</option>
        <option value="rice">rice</option>
        <option value="schistosoma2">schistosoma2</option>
        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
    </xml>

    <xml name="lineages">
        <option value="acidobacteria_odb10">Acidobacteria</option>
        <option value="aconoidasida_odb10">Aconoidasida</option>
        <option value="actinobacteria_class_odb10">Actinobacteria class</option>
        <option value="actinobacteria_phylum_odb10">Actinobacteria phylum</option>
        <option value="actinopterygii_odb10">Actinopterygii</option>
        <option value="agaricales_odb10">Agaricales</option>
        <option value="agaricomycetes_odb10">Agaricomycetes</option>
        <option value="alphaproteobacteria_odb10">Alphaproteobacteria</option>
        <option value="alteromonadales_odb10">Alteromonadales</option>
        <option value="alveolata_odb10">Alveolata</option>
        <option value="apicomplexa_odb10">Apicomplexa</option>
        <option value="aquificae_odb10">Aquificae</option>
        <option value="arachnida_odb10">Arachnida</option>
        <option value="archaea_odb10">Archaea</option>
        <option value="arthropoda_odb10">Arthropoda</option>
        <option value="ascomycota_odb10">Ascomycota</option>
        <option value="aves_odb10">Aves</option>
        <option value="bacillales_odb10">Bacillales</option>
        <option value="bacilli_odb10">Bacilli</option>
        <option value="bacteria_odb10">Bacteria</option>
        <option value="bacteroidales_odb10">Bacteroidales</option>
        <option value="bacteroidetes-chlorobi_group_odb10">Bacteroidetes-chlorobi group</option>
        <option value="bacteroidetes_odb10">Bacteroidetes</option>
        <option value="bacteroidia_odb10">Bacteroidia</option>
        <option value="basidiomycota_odb10">Basidiomycota</option>
        <option value="betaproteobacteria_odb10">Betaproteobacteria</option>
        <option value="boletales_odb10">Boletales</option>
        <option value="brassicales_odb10">Brassicales</option>
        <option value="burkholderiales_odb10">Burkholderiales</option>
        <option value="campylobacterales_odb10">Campylobacterales</option>
        <option value="capnodiales_odb10">Capnodiales</option>
        <option value="carnivora_odb10">Carnivora</option>
        <option value="cellvibrionales_odb10">Cellvibrionales</option>
        <option value="cetartiodactyla_odb10">Cetartiodactyla</option>
        <option value="chaetothyriales_odb10">Chaetothyriales</option>
        <option value="chlamydiae_odb10">Chlamydiae</option>
        <option value="chlorobi_odb10">Chlorobi</option>
        <option value="chloroflexi_odb10">Chloroflexi</option>
        <option value="chlorophyta_odb10">Chlorophyta</option>
        <option value="chromatiales_odb10">Chromatiales</option>
        <option value="chroococcales_odb10">Chroococcales</option>
        <option value="clostridia_odb10">Clostridia</option>
        <option value="clostridiales_odb10">Clostridiales</option>
        <option value="coccidia_odb10">Coccidia</option>
        <option value="coriobacteriales_odb10">Coriobacteriales</option>
        <option value="coriobacteriia_odb10">Coriobacteriia</option>
        <option value="corynebacteriales_odb10">Corynebacteriales</option>
        <option value="cyanobacteria_odb10">Cyanobacteria</option>
        <option value="cyprinodontiformes_odb10">Cyprinodontiformes</option>
        <option value="cytophagales_odb10">Cytophagales</option>
        <option value="cytophagia_odb10">Cytophagia</option>
        <option value="delta-epsilon-subdivisions_odb10">Delta-epsilon-subdivisions</option>
        <option value="deltaproteobacteria_odb10">Deltaproteobacteria</option>
        <option value="desulfobacterales_odb10">Desulfobacterales</option>
        <option value="desulfovibrionales_odb10">Desulfovibrionales</option>
        <option value="desulfurococcales_odb10">Desulfurococcales</option>
        <option value="desulfuromonadales_odb10">Desulfuromonadales</option>
        <option value="diptera_odb10">Diptera</option>
        <option value="dothideomycetes_odb10">Dothideomycetes</option>
        <option value="embryophyta_odb10">Embryophyta</option>
        <option value="endopterygota_odb10">Endopterygota</option>
        <option value="enterobacterales_odb10">Enterobacterales</option>
        <option value="entomoplasmatales_odb10">Entomoplasmatales</option>
        <option value="epsilonproteobacteria_odb10">Epsilonproteobacteria</option>
        <option value="euarchontoglires_odb10">Euarchontoglires</option>
        <option value="eudicots_odb10">Eudicots</option>
        <option value="euglenozoa_odb10">Euglenozoa</option>
        <option value="eukaryota_odb10">Eukaryota</option>
        <option value="eurotiales_odb10">Eurotiales</option>
        <option value="eurotiomycetes_odb10">Eurotiomycetes</option>
        <option value="euryarchaeota_odb10">Euryarchaeota</option>
        <option value="eutheria_odb10">Eutheria</option>
        <option value="fabales_odb10">Fabales</option>
        <option value="firmicutes_odb10">Firmicutes</option>
        <option value="flavobacteriales_odb10">Flavobacteriales</option>
        <option value="flavobacteriia_odb10">Flavobacteriia</option>
        <option value="fungi_odb10">Fungi</option>
        <option value="fusobacteria_odb10">Fusobacteria</option>
        <option value="fusobacteriales_odb10">Fusobacteriales</option>
        <option value="gammaproteobacteria_odb10">Gammaproteobacteria</option>
        <option value="glires_odb10">Glires</option>
        <option value="glomerellales_odb10">Glomerellales</option>
        <option value="halobacteria_odb10">Halobacteria</option>
        <option value="halobacteriales_odb10">Halobacteriales</option>
        <option value="haloferacales_odb10">Haloferacales</option>
        <option value="helotiales_odb10">Helotiales</option>
        <option value="hemiptera_odb10">Hemiptera</option>
        <option value="hymenoptera_odb10">Hymenoptera</option>
        <option value="hypocreales_odb10">Hypocreales</option>
        <option value="insecta_odb10">Insecta</option>
        <option value="lactobacillales_odb10">Lactobacillales</option>
        <option value="laurasiatheria_odb10">Laurasiatheria</option>
        <option value="legionellales_odb10">Legionellales</option>
        <option value="leotiomycetes_odb10">Leotiomycetes</option>
        <option value="lepidoptera_odb10">Lepidoptera</option>
        <option value="liliopsida_odb10">Liliopsida</option>
        <option value="mammalia_odb10">Mammalia</option>
        <option value="metazoa_odb10">Metazoa</option>
        <option value="methanobacteria_odb10">Methanobacteria</option>
        <option value="methanococcales_odb10">Methanococcales</option>
        <option value="methanomicrobia_odb10">Methanomicrobia</option>
        <option value="methanomicrobiales_odb10">Methanomicrobiales</option>
        <option value="micrococcales_odb10">Micrococcales</option>
        <option value="microsporidia_odb10">Microsporidia</option>
        <option value="mollicutes_odb10">Mollicutes</option>
        <option value="mollusca_odb10">Mollusca</option>
        <option value="mucorales_odb10">Mucorales</option>
        <option value="mucoromycota_odb10">Mucoromycota</option>
        <option value="mycoplasmatales_odb10">Mycoplasmatales</option>
        <option value="natrialbales_odb10">Natrialbales</option>
        <option value="neisseriales_odb10">Neisseriales</option>
        <option value="nematoda_odb10">Nematoda</option>
        <option value="nitrosomonadales_odb10">Nitrosomonadales</option>
        <option value="nostocales_odb10">Nostocales</option>
        <option value="oceanospirillales_odb10">Oceanospirillales</option>
        <option value="onygenales_odb10">Onygenales</option>
        <option value="oscillatoriales_odb10">Oscillatoriales</option>
        <option value="passeriformes_odb10">Passeriformes</option>
        <option value="pasteurellales_odb10">Pasteurellales</option>
        <option value="planctomycetes_odb10">Planctomycetes</option>
        <option value="plasmodium_odb10">Plasmodium</option>
        <option value="pleosporales_odb10">Pleosporales</option>
        <option value="poales_odb10">Poales</option>
        <option value="polyporales_odb10">Polyporales</option>
        <option value="primates_odb10">Primates</option>
        <option value="propionibacteriales_odb10">Propionibacteriales</option>
        <option value="proteobacteria_odb10">Proteobacteria</option>
        <option value="pseudomonadales_odb10">Pseudomonadales</option>
        <option value="rhizobiales_odb10">Rhizobiales</option>
        <option value="rhizobium-agrobacterium_group_odb10">Rhizobium-agrobacterium group</option>
        <option value="rhodobacterales_odb10">Rhodobacterales</option>
        <option value="rhodospirillales_odb10">Rhodospirillales</option>
        <option value="rickettsiales_odb10">Rickettsiales</option>
        <option value="saccharomycetes_odb10">Saccharomycetes</option>
        <option value="sauropsida_odb10">Sauropsida</option>
        <option value="selenomonadales_odb10">Selenomonadales</option>
        <option value="solanales_odb10">Solanales</option>
        <option value="sordariomycetes_odb10">Sordariomycetes</option>
        <option value="sphingobacteriia_odb10">Sphingobacteriia</option>
        <option value="sphingomonadales_odb10">Sphingomonadales</option>
        <option value="spirochaetales_odb10">Spirochaetales</option>
        <option value="spirochaetes_odb10">Spirochaetes</option>
        <option value="spirochaetia_odb10">Spirochaetia</option>
        <option value="stramenopiles_odb10">Stramenopiles</option>
        <option value="streptomycetales_odb10">Streptomycetales</option>
        <option value="streptosporangiales_odb10">Streptosporangiales</option>
        <option value="sulfolobales_odb10">Sulfolobales</option>
        <option value="synechococcales_odb10">Synechococcales</option>
        <option value="synergistetes_odb10">Synergistetes</option>
        <option value="tenericutes_odb10">Tenericutes</option>
        <option value="tetrapoda_odb10">Tetrapoda</option>
        <option value="thaumarchaeota_odb10">Thaumarchaeota</option>
        <option value="thermoanaerobacterales_odb10">Thermoanaerobacterales</option>
        <option value="thermoplasmata_odb10">Thermoplasmata</option>
        <option value="thermoproteales_odb10">Thermoproteales</option>
        <option value="thermoprotei_odb10">Thermoprotei</option>
        <option value="thermotogae_odb10">Thermotogae</option>
        <option value="thiotrichales_odb10">Thiotrichales</option>
        <option value="tissierellales_odb10">Tissierellales</option>
        <option value="tissierellia_odb10">Tissierellia</option>
        <option value="tremellomycetes_odb10">Tremellomycetes</option>
        <option value="verrucomicrobia_odb10">Verrucomicrobia</option>
        <option value="vertebrata_odb10">Vertebrata</option>
        <option value="vibrionales_odb10">Vibrionales</option>
        <option value="viridiplantae_odb10">Viridiplantae</option>
        <option value="xanthomonadales_odb10">Xanthomonadales</option>
    </xml>
</macros>