Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder
changeset 12:13d2d138e0e2 draft default tip
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_phylogeny_builder commit f1998b1af463af68d71cb4697fc4e1fa471cdd5a"
| author | greg |
|---|---|
| date | Tue, 20 Jul 2021 20:29:00 +0000 |
| parents | 800402ed6eb7 |
| children | |
| files | .shed.yml gene_family_phylogeny_builder.xml plant_tribes_scaffolds.loc test-data/3722.faa.aln test-data/3722.faa.aln.tree test-data/plant_tribes_scaffolds.loc test-data/tool-data/plant_tribes/scaffolds/README.txt tool-data/plant_tribes_scaffolds.loc.sample tool_data_table_conf.xml.test |
| diffstat | 9 files changed, 273 insertions(+), 294 deletions(-) [+] |
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--- a/.shed.yml Thu Sep 06 09:40:44 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -name: plant_tribes_gene_family_phylogeny_builder -owner: greg -description: | - Contains a tool that creates multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups. -homepage_url: https://github.com/dePamphilis/PlantTribes -long_description: | - This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of - complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic - analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the - GeneFamilyAligner tool. -remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_phylogeny_builder -type: unrestricted -categories: -- Phylogenetics
--- a/gene_family_phylogeny_builder.xml Thu Sep 06 09:40:44 2018 -0400 +++ b/gene_family_phylogeny_builder.xml Tue Jul 20 20:29:00 2021 +0000 @@ -1,10 +1,10 @@ -<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.1" profile="18.09"> +<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.4.1" profile="18.09"> <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.0.3">plant_tribes_gene_family_phylogeny_builder</requirement> + <requirement type="package" version="1.0.4">plant_tribes_gene_family_phylogeny_builder</requirement> </requirements> <code file="get_clustering_methods.py"/> <command detect_errors="exit_code"><![CDATA[ @@ -94,7 +94,7 @@ </param> <param name="tree_inference" value="fasttree"/> <output_collection name="tree" type="list"> - <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="newick"/> + <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="newick" compare="contains"/> </output_collection> </test> </tests>
--- a/plant_tribes_scaffolds.loc Thu Sep 06 09:40:44 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -## Plant Tribes scaffolds -#Value Name Path Description -22Gv1.1 22Gv1.1 ${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- a/test-data/3722.faa.aln Thu Sep 06 09:40:44 2018 -0400 +++ b/test-data/3722.faa.aln Tue Jul 20 20:29:00 2021 +0000 @@ -1,312 +1,304 @@ >gnl_Glyma1.01_PACid_16266208 ----MANE-------------------------------------------------GKKS -NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG ---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- -----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM -NFGK---AENSSVFDASY------QNFCFG-VN--QLQDIKKGK---GGILGGGGRSRHR -SGRKQKMFY-GHDV-------------------------- +---MANE----------------------------------------------GKKSNNF +YSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSHTKSNENG--E +ESFEELQ------QLFEDMFQADI--GL---D--GGPSL-----------------ASSD +SSTSSA------------------YMTYSESSS---------SNKRNSS-EMNFGK---A +ENSSVFDASY--------------QNFCFG-VN--QLQDIKKGK---GGILGGGGR-SRH +RSGRKQKMFY-GHDV-------------------------- >gnl_Glyma1.01_PACid_16266209 ----MANE-------------------------------------------------GKKS -NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG ---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- -----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM -NFGK---AENSSVFDASY------QNFCFG-TG--EPTPRYKEG--------KGGNSRRR -R--------------------------------------- +---MANE----------------------------------------------GKKSNNF +YSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSHTKSNENG--E +ESFEELQ------QLFEDMFQADI--GL---D--GGPSL-----------------ASSD +SSTSSA------------------YMTYSESSS---------SNKRNSS-EMNFGK---A +ENSSVFDASY--------------QNFCFG-TG--EPTPRYKEG--------KGGN-SRR +RR--------------------------------------- >gnl_Glyma1.01_PACid_16266210 ----MANE-------------------------------------------------GKKS -NNFYSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSHTKSNENG ---EESFEELQ------QLFEDMFQADI--GL----------DGGPSL------------- -----ASSDSSTSSA------------------YMTYSESSS---------SNKRNSS-EM -NFGK---AENSSVFDASY------QNFCFG-VG--HVNYHYQ------------------ ----------------------------------------- +---MANE----------------------------------------------GKKSNNF +YSILGLSKECTELELKNAYRKLAKKWHPDRCSATG---NLELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSHTKSNENG--E +ESFEELQ------QLFEDMFQADI--GL---D--GGPSL-----------------ASSD +SSTSSA------------------YMTYSESSS---------SNKRNSS-EMNFGK---A +ENSSVFDASY--------------QNFCFG-VG--HVNYHYQ------------------ +----------------------------------------- >gnl_Glyma1.01_PACid_16301083 ----MADE-------------------------------------------------GNKS -NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG ---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- -----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM -NFGK---AENSSVFDAGY------QNFCFG-VN--QLQDIKKKK---GGIL-GGGRSRHR -NGRKQNMSY-GHDVSSNDYPGISTK--------------- +---MADE----------------------------------------------GNKSNNF +YSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSQTKSNENG--E +ESFEELQ------QLFEDMFEADI--GL---D--GGPSL-----------------ASSD +CSTSSA------------------YMTYSESSS---------SNKHNSS-EMNFGK---A +ENSSVFDAGY--------------QNFCFG-VN--QLQDIKKKK---GGIL-GGGR-SRH +RNGRKQNMSY-GHDVSSNDYPGISTK--------------- >gnl_Glyma1.01_PACid_16301085 ----MADE-------------------------------------------------GNKS -NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG ---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- -----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM -NFGK---AENSSVFDAGY------QNFCFG-VG--HVNYHYQ------------------ ----------------------------------------- +---MADE----------------------------------------------GNKSNNF +YSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSQTKSNENG--E +ESFEELQ------QLFEDMFEADI--GL---D--GGPSL-----------------ASSD +CSTSSA------------------YMTYSESSS---------SNKHNSS-EMNFGK---A +ENSSVFDAGY--------------QNFCFG-VG--HVNYHYQ------------------ +----------------------------------------- >gnl_Glyma1.01_PACid_16301084 ----MADE-------------------------------------------------GNKS -NNFYSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAY -S------VLSDANKRLMYDVGVYDS--------DDDENGMGDFLDEMLTMMSQTKSNENG ---EESFEELQ------QLFEDMFEADI--GL----------DGGPSL------------- -----ASSDCSTSSA------------------YMTYSESSS---------SNKHNSS-EM -NFGK---AENSSVFDAGY------QNFCFG-TG--EPTPRYKEE--------KGGNSRRR ----------------------------------------- +---MADE----------------------------------------------GNKSNNF +YSILGLKKECTELELKNAYRKLAKKWHPDRCSATG---NSELVEEAKKKFQEIREAYS-- +----VLSDANKRLMYDVGVYDSDD--------DENGMGDFLDEMLTMMSQTKSNENG--E +ESFEELQ------QLFEDMFEADI--GL---D--GGPSL-----------------ASSD +CSTSSA------------------YMTYSESSS---------SNKHNSS-EMNFGK---A +ENSSVFDAGY--------------QNFCFG-TG--EPTPRYKEE--------KGGN-SRR +R---------------------------------------- >gnl_Medtr3.5_Medtr8g022310.1 ----MANE-------------------------------------------------GNKS -NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY -S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG ---EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- -----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM -NFGK---AEDSSSFGANY------QNFCFG-MK--HLQEDVEKE--KGGILEGGGSKKQR -KGRKQKISC-GH-VSSNDHPGISAN--------------- +---MANE----------------------------------------------GNKSNDF +YAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAYS-- +----VLSDSNKRLMYDVGVYDSDD--------DENGMGDFLNEMVTMMSQTKSNENG--E +ESFEELQ------QLFDDMFQADI--GL---N--GSTSL-----------------NASG +CSTSST------------------FMTFSESSN---------SNKRNST-QMNFGK---A +EDSSSFGANY--------------QNFCFG-MK--HLQEDVEKE--KGGILEGGGS-KKQ +RKGRKQKISC-GH-VSSNDHPGISAN--------------- >gnl_Medtr3.5_Medtr8g022310.2 ----MANE-------------------------------------------------GNKS -NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY -S------VLSDSNKRLMYDVGVYDS--------DDDENGMGDFLNEMVTMMSQTKSNENG ---EESFEELQ------QLFDDMFQADI--GL----------NGSTSL------------- -----NASGCSTSST------------------FMTFSESSN---------SNKRNST-QM -NFGK---AEDSSSFGANY------QNFCFG-VN--LVNYHYQ------------------ ----------------------------------------- +---MANE----------------------------------------------GNKSNDF +YAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAYS-- +----VLSDSNKRLMYDVGVYDSDD--------DENGMGDFLNEMVTMMSQTKSNENG--E +ESFEELQ------QLFDDMFQADI--GL---N--GSTSL-----------------NASG +CSTSST------------------FMTFSESSN---------SNKRNST-QMNFGK---A +EDSSSFGANY--------------QNFCFG-VN--LVNYHYQ------------------ +----------------------------------------- >gnl_Musac1.0_GSMUA_Achr6T31040_001 ----MAAE-------------------------------------------------EDKS -GDFYAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAY -S------VLSDSNKRFLYDVGVYDND------DDNDENGMGDFIGEMLEMMSQTKPNENS ---QDSFQELQ------ELFVEMFQDDL--DAG---------FGGSIFH-DCPWAQP---- ----TNGQDCWTSSG------------------LHFANGRSK--------CGNKRGNS-AV -NLGK----VNLEELEHGT------SDFYFG-LN--DAAQPSQGKGGS--------NNKRR -NGRKQKVSS-NHDVSS------------------------ +---MAAE----------------------------------------------EDKSGDF +YAVLGLRKECSETELRNAYKKLAMRWHPDKCLASG---NAQIVGEAKEKFQEIQKAYS-- +----VLSDSNKRFLYDVGVYDNDD------DNDENGMGDFIGEMLEMMSQTKPNENS--Q +DSFQELQ------ELFVEMFQDDL--DAG--F--GGSIFH---DCPWAQP-----TNGQD +CWTSSG------------------LHFANGRSK--------CGNKRGNS-AVNLGK---- +VNLEELEHGT--------------SDFYFG-LN--DAAQPSQGKGGS--------N-NKR +RNGRKQKVSS-NHDVSS------------------------ >gnl_Musac1.0_GSMUA_Achr9T18140_001 ----MAAG-------------------------------------------------EEKI -GDFYTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASG---NHRRMEEAKEKFQEIQKAY -S------VLSDSSKRFLYDVGIYDNE------DDNDEKGMGDFIGEIAQMMSQTKSGENG ---HDSFEELQ------RMFLDMFQDDL--DAG---------FGDSSIH-SGPQARP---- ----TDGLNCSMPSG------------------LQFADGGNN--------GSNKRGNS-EK ---------AKLDGLENSS------TGFCFG-LN--DAGQSSKGKGSA--------NSKRR -NGRKQKVSS-KHDVSSSD-AEVSF---------------- +---MAAG----------------------------------------------EEKIGDF +YTVLGLRKECSEAELRIAYKKLAMRWHPDKCSASG---NHRRMEEAKEKFQEIQKAYS-- +----VLSDSSKRFLYDVGIYDNED------DNDEKGMGDFIGEIAQMMSQTKSGENG--H +DSFEELQ------RMFLDMFQDDL--DAG--F--GDSSIH---SGPQARP-----TDGLN +CSMPSG------------------LQFADGGNN--------GSNKRGNS-EK-------- +AKLDGLENSS--------------TGFCFG-LN--DAGQSSKGKGSA--------N-SKR +RNGRKQKVSS-KHDVSSSD-AEVSF---------------- >gnl_Musac1.0_GSMUA_Achr8T23700_001 ----MASD-------------------------------------------------MDAS -GDFYSVLGLKKECSEAELRNAYKKLALKWHPDKCSASG---NEIRMKEAKQQFQEIQKAY -S------VLSDSNKRFLYDVGAYDKD------DDKDEEGMVEFLGEMAQMMRQTKCCGSG ---QESFEQLQ------QMFVEMFHDDL--DAG---------F------------------ ---------CGHSSA---------------------TSGAAS--------CGNKRDNS-AM -DSGK----RKPDELDPAA------IGFCLG-TK--DAGQSSKGRGS---------NSKRR -NRRKQKASS-KHDNSSHN-AKVSA---------------- +---MASD----------------------------------------------MDASGDF +YSVLGLKKECSEAELRNAYKKLALKWHPDKCSASG---NEIRMKEAKQQFQEIQKAYS-- +----VLSDSNKRFLYDVGAYDKDD------DKDEEGMVEFLGEMAQMMRQTKCCGSG--Q +ESFEQLQ------QMFVEMFHDDL--DAG--F---------------------------- +CGHSSA---------------------TSGAAS--------CGNKRDNS-AMDSGK---- +RKPDELDPAA--------------IGFCLG-TK--DAGQSSKGRGS---------N-SKR +RNRRKQKASS-KHDNSSHN-AKVSA---------------- >gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001 ----MEGD-------------------------------------------------EEKS -GDFYAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASG---NKIRMDKAKEKFQEIQKAY -S------VLSDSNKRFLYDVGVYDKD------DEEDEEGMGDFIGEIAQMMSQSKPSGSG ---HESLEELH------RQVVEMFLDEL--DAGD-------RFSSANQ------------- -----GASSCDGRDD----------------------------------GGGNKRGNW-AV -DWGK----EKLNELGPGT------GGFCFG-VS------------------------RRV -HSFDLMIDV-VHLIHSDL-------------------TLE +---MEGD----------------------------------------------EEKSGDF +YAVLGLKKEGSMAELKNAYKKLAMKWHPDKCPASG---NKIRMDKAKEKFQEIQKAYS-- +----VLSDSNKRFLYDVGVYDKDD------EEDEEGMGDFIGEIAQMMSQSKPSGSG--H +ESLEELH------RQVVEMFLDEL--DAGDRF--SSANQ-----------------GASS +CDGRDD----------------------------------GGGNKRGNW-AVDWGK---- +EKLNELGPGT--------------GGFCFG-VS-------------------------RR +VHSFDLMIDV-VHLIHSDL-------------TLE------ >gnl_Orysa6.0_PACid_16843526 ----MADGG-------------------------------------EKC-RDAAG-EGGGG -GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY -S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- ---QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT -SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM -DSGK-PPRASEVGSGQSQ------SGFCFG-KS--DAKQAAKTRSGNT-------ASRRR -NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +---MADGGE----------------------------------KC-RDAAG-EGGGGGDL +YAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAYS-- +----VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR----Q +ESFKELQ------QLFVDMFQADL--DSG--F--CNGPSKCYHTQAQSQTRTSSTSPSMS +PSPPPP------------------VATEAESPS------CNGINKRGSS-AMDSGK-PPR +ASEVGSGQSQ--------------SGFCFG-KS--DAKQAAKTRSGNT-------A-SRR +RNGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA >gnl_Orysa6.0_PACid_16843528 ----MADGG-------------------------------------EKC-RDAAG-EGGGG -GDLYAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAY -S------VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR-- ---QESFKELQ------QLFVDMFQADL--DSG---------FCNGPSKCYHTQAQSQTRT -SSTSPSMSPSPPPP------------------VATEAESPS------CNGINKRGSS-AM -DSGK-PPRASEVGSGQSQ------SGFCFGQKS--DAKQAAKTRSGNT-------ASRRR -NGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA +---MADGGE----------------------------------KC-RDAAG-EGGGGGDL +YAVLGLKKECSDADLKLAYRKLAMRWHPDKCSSSS---SAKHMEEAKEKFQEIQGAYS-- +----VLSDSNKRFLYDVGVYDDDD----NDDDNLQGMGDFIGEMAQMMSQARPTR----Q +ESFKELQ------QLFVDMFQADL--DSG--F--CNGPSKCYHTQAQSQTRTSSTSPSMS +PSPPPP------------------VATEAESPS------CNGINKRGSS-AMDSGK-PPR +ASEVGSGQSQ--------------SGFCFGQKS--DAKQAAKTRSGNT-------A-SRR +RNGRKQKVSS-KHDVSSEDEMPGSQW-----------HGVA >gnl_Poptr2.2_PACid_18217800 ----MANGGE----------------------------------------------DKWKS -NDLYQVLGLNKECTDTELRSAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY -S------VLSDTNKRFLYDVGVDDS--------DDDENGMGDFLNEMAVMMSQTKPSENM ---EESLEELQ------ELFDEMFQEDL--HS----------FGIDSQ------------- -----AAPSC--PPS------------------YVSYSESSN--------SNNKRVSA-DM -NLGK-TKVDDSSSFNSHF------EKFCLG-T-----------GGTAATFQEGEGGSKRR -NSRRSQRQT-KARQETKSFFGL------------------ +---MANGGE-------------------------------------------DKWKSNDL +YQVLGLNKECTDTELRSAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAYS-- +----VLSDTNKRFLYDVGVDDSDD--------DENGMGDFLNEMAVMMSQTKPSENM--E +ESLEELQ------ELFDEMFQEDL--HS---F--GIDSQ-----------------AAPS +C--PPS------------------YVSYSESSN--------SNNKRVSA-DMNLGK-TKV +DDSSSFNSHF--------------EKFCLG-T-----------GGTAATFQEGEGG-SKR +RNSRRSQRQT-KARQETKSFFGL------------------ >gnl_Poptr2.2_PACid_18234651 ----MENGGE----------------------------------------------EKGKS -NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY -S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV ---EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- -----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM -NLKK-TKVDDSSGFNSHV------EKFCLG-V-----------SGTPAIFQEGE-GSKRR -SSRRNRR--------------------------------- +---MENGGE-------------------------------------------EKGKSNDF +YQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAYS-- +----VLSDTNKRFLYDVGVYDSED--------DENGMGGFMNEMAAMMSQTKPHENV--E +ESFEELQ------GLFEEMFQEDL--DS---F--GIACQ-----------------ATT- +------------------------CVSYSESSN--------SNDKRVSV-DMNLKK-TKV +DDSSGFNSHV--------------EKFCLG-V-----------SGTPAIFQEGE-G-SKR +RSSRRNRR--------------------------------- >gnl_Poptr2.2_PACid_18234649 -MLRMENGGE----------------------------------------------EKGKS -NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY -S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV ---EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- -----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM -NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER -KGRKQEVSS-GYDVSSHD-HGISAS--------------- +MLRMENGGE-------------------------------------------EKGKSNDF +YQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAYS-- +----VLSDTNKRFLYDVGVYDSED--------DENGMGGFMNEMAAMMSQTKPHENV--E +ESFEELQ------GLFEEMFQEDL--DS---F--GIACQ-----------------ATT- +------------------------CVSYSESSN--------SNDKRVSV-DMNLKK-TKV +DDSSGFNSHV--------------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-G-GRE +RKGRKQEVSS-GYDVSSHD-HGISAS--------------- >gnl_Poptr2.2_PACid_18234650 ----MENGGE----------------------------------------------EKGKS -NDFYQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAY -S------VLSDTNKRFLYDVGVYDS--------EDDENGMGGFMNEMAAMMSQTKPHENV ---EESFEELQ------GLFEEMFQEDL--DS----------FGIACQ------------- -----ATT-------------------------CVSYSESSN--------SNDKRVSV-DM -NLKK-TKVDDSSGFNSHV------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-GGRER -KGRKQEVSS-GYDVSSHD-HGISAS--------------- +---MENGGE-------------------------------------------EKGKSNDF +YQVLGLNKDCTATELRNAYKKLALKWHPDRCSASE---NSRFVDEAKKKFQTIQQAYS-- +----VLSDTNKRFLYDVGVYDSED--------DENGMGGFMNEMAAMMSQTKPHENV--E +ESFEELQ------GLFEEMFQEDL--DS---F--GIACQ-----------------ATT- +------------------------CVSYSESSN--------SNDKRVSV-DMNLKK-TKV +DDSSGFNSHV--------------EKFCLG-VE--HQQSFKKGKGVRGGVQGGT-G-GRE +RKGRKQEVSS-GYDVSSHD-HGISAS--------------- >gnl_Soltu3.4_PGSC0003DMP400016105 ----M-------------------------------------------------------G -NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY -S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ ---EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- -----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM -KSGK--------GDSCQF------QGFCEG-T-----------GGASGKSNERE-RSRRK -NSKSGRKQ-------------------------------- +---M----------------------------------------------------GNDY +YAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAYS-- +----VLSDANKRFLYDVGVYDSGD------DDDENGMGDFLNEMAAMMSQNKSNENQ--E +ETFEELQ------DMFDEIFNSDN--GM-------SSSS-----------------SSSS +RTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EMKSGK---- +----GDSCQF--------------QGFCEG-T-----------GGASGKSNERE-R-SRR +KNSKSGRKQ-------------------------------- >gnl_Soltu3.4_PGSC0003DMP400016106 ----M-------------------------------------------------------G -NDYYAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAY -S------VLSDANKRFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ ---EETFEELQ------DMFDEIFNSDN--GM------------SSSS------------- -----SSSSRTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EM -KSGK--------GDSCQF------QGFCEG-VE--HLEKAMKENGVGGKIPRVD-GSNRM -DAKRQKVLS------------------------------- +---M----------------------------------------------------GNDY +YAVLGLKKECTETELRNAYKKLALKWHPDRCSASG---NSKFVDEAKKKFQAIQEAYS-- +----VLSDANKRFLYDVGVYDSGD------DDDENGMGDFLNEMAAMMSQNKSNENQ--E +ETFEELQ------DMFDEIFNSDN--GM-------SSSS-----------------SSSS +RTGTPS------------------MCSTTSSTSSSET-FFTFSNKRSSG-EMKSGK---- +----GDSCQF--------------QGFCEG-VE--HLEKAMKENGVGGKIPRVD-G-SNR +MDAKRQKVLS------------------------------- >gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329 ----MAPR-------------------------------------------------GEKD -SDFYAILGLKKECSASDLRNAYKRLALRWHPDRCSASG---NTKFVEECKKKFQAIQQAY -S------VLSDANKRFLYDVGAYGS--------DDDDQGMGEFLGEMAVMMSQTKPSEKG ---PESFEDLQ------NLFQEMFERDL--DM----------FKSSTSH------------ -----NNNNDNNNNN------------------HRSSDNNNCSSVH-CFSNTNKRNCS-DM -NAGE-ASEVGRFAFSCYATEFLHKQTFSVG-AD------DVRSES----------SNKRR -NGRKQKSTS-SSRKS------------------------- +---MAPR----------------------------------------------GEKDSDF +YAILGLKKECSASDLRNAYKRLALRWHPDRCSASG---NTKFVEECKKKFQAIQQAYS-- +----VLSDANKRFLYDVGAYGSDD--------DDQGMGEFLGEMAVMMSQTKPSEKG--P +ESFEDLQ------NLFQEMFERDL--DM---F--KSSTSH----------------NNNN +DNNNNN------------------HRSSDNNNCSSVH-CFSNTNKRNCS-DMNAGE-ASE +VGRFAFSCYA--------TEFLHKQTFSVG-AD------DVRSES----------S-NKR +RNGRKQKSTS-SSRKS------------------------- >gnl_Aquco1.0_PACid_18141277 ----MAS--------------------------------------------------EEEA -SDFYKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASG---NSKFVEEAKKNFQAIQEAY -S------VLSDEQKRFMYDVGVYDKD------DDDENEDMGDFLGEMMSMMKQENTSADG ---QQSFEDLQ------NLFQEMVQNDK--EF----------YNPASQ------------- -----NSSIYNASNNMFSFSNNENLNNASNNTFSSFYNENLN--------SSNKKSCS-SM -SAEN--TKVDFNMESLDF------RSFSIG-LE--GGTSFQNSKGRG--------VTGRR -TGRKQKGSS-CNDMSSHD-SKILA---------------- +---MAS-----------------------------------------------EEEASDF +YKVLGLKNNCSSLELRNAYKKLALKWHPDRCAASG---NSKFVEEAKKNFQAIQEAYS-- +----VLSDEQKRFMYDVGVYDKDD------DDENEDMGDFLGEMMSMMKQENTSADG--Q +QSFEDLQ------NLFQEMVQNDK--EF---Y--NPASQ-----------------NSSI +YNASNNMFSFSNNENLNNASNNTFSSFYNENLN--------SSNKKSCS-SMSAEN--TK +VDFNMESLDF--------------RSFSIG-LE--GGTSFQNSKGRG--------V-TGR +RTGRKQKGSS-CNDMSSHD-SKILA---------------- >gnl_Arath10_AT3G14200.1 ----MASSN-----------------------------------------------SEKIN -ENLYAVLGLKKECSKTELRSAYKKLALRWHPDRCSS------MEFVEEAKKKFQAIQEAY -S------VLSDSNKRFLYDVGAYNTD------DDDDQNGMGDFLNEMATMMNQSKPSDNN --TGDSFEQLQ------DLFNEMFQGDA--AA----------FPSS--------------- -------SSCSTSNF------------------TSSRSFVFD--------TNSQRSSSFAT -SSMG--MNNDPFGYDPRA------HSFSLG-VD--HQQEFKKGKN----------NGGRR -NRRKNNVPSAGHETSSSNNYGVPTS--------------- +---MASSN--------------------------------------------SEKINENL +YAVLGLKKECSKTELRSAYKKLALRWHPDRCSS------MEFVEEAKKKFQAIQEAYS-- +----VLSDSNKRFLYDVGAYNTDD------DDDQNGMGDFLNEMATMMNQSKPSDNN-TG +DSFEQLQ------DLFNEMFQGDA--AA---F--PSS---------------------SS +CSTSNF------------------TSSRSFVFD--------TNSQRSSSFATSSMG--MN +NDPFGYDPRA--------------HSFSLG-VD--HQQEFKKGKN----------N-GGR +RNRRKNNVPSAGHETSSSNNYGVPTS--------------- >gnl_Bradi1.2_Bradi3g60090.1 ----MATGG-------------------------------------DKCGGKPAA-AGVGG -GDLYSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSS---STKHMEEAKEKFQEIQGAY -S------VLSDANKRFLYDVGVYEEHEE---EDDDTLQGMGDFLGEMAHMMSQTQPAR-- ---QESFEELQ------QLFVDMFQSDI--ESG---------FCNGPAK-DHDPVQRQTRT -FSTPPSPSPSPPPP------------------LATVDEAAS------CNGINKRGSS-AM -GSGK-PPRAGEVSGGHGQ------SEFCFG-MS--DAKQAPKARGGN--------ASRRR -NGQKQKLSS-KHDVSSGDEMPRP-------------HAAV +---MATGGD----------------------------------KCGGKPAA-AGVGGGDL +YSVLGVNKECSDADLKVAYRKLAMRWHPDRCSSSS---STKHMEEAKEKFQEIQGAYS-- +----VLSDANKRFLYDVGVYEEHEE---EDDDTLQGMGDFLGEMAHMMSQTQPAR----Q +ESFEELQ------QLFVDMFQSDI--ESG--F--CNGPAK-DHDPVQRQTRTFSTPPSPS +PSPPPP------------------LATVDEAAS------CNGINKRGSS-AMGSGK-PPR +AGEVSGGHGQ--------------SEFCFG-MS--DAKQAPKARGGN--------A-SRR +RNGQKQKLSS-KHDVSSGDEMPRP-------------HAAV >gnl_Carpa1.181_PACid_16420351 ----MADG------------------------------------------------EDKNN -SDLYAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASG---NSMFVEEAKKKFQAIQEAY -S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAAMMSQTKPNENG -NAQESFEELQ------ELFQEMFQGDMGFNT----------FGSSSQP------------ -----TTSSCSASSA------------------YATCSETSN-------PNNNKRNSS-EM -NYGK-KKVDDSSGFHAHF------QTFCLG-VE--QQQDFKKGKEARGGIRGKP-GGSRR -QGRKQKVSS-RHNVSSND-LGISAS--------------- +---MADG---------------------------------------------EDKNNSDL +YAVLGLNKECTPAELRNAYKKLAMRWHPDRCSASG---NSMFVEEAKKKFQAIQEAYS-- +----VLSDANKRFLYDVGAYESDD--------DENGMGDFLNEMAAMMSQTKPNENGNAQ +ESFEELQ------ELFQEMFQGDMGFNT---F--GSSSQP----------------TTSS +CSASSA------------------YATCSETSN-------PNNNKRNSS-EMNYGK-KKV +DDSSGFHAHF--------------QTFCLG-VE--QQQDFKKGKEARGGIRGKP-G-GSR +RQGRKQKVSS-RHNVSSND-LGISAS--------------- >gnl_Frave2.0_gene05408 ----MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNR---RMEEKG -NDFYAVMGLKKECSDSELRNAYKKLALIWHPDRCSASG---NSKFVEEAKKKFQDIQQAY -S------VLSDANKRFLYDVGAYES--------DDDENGMGDFLNEMAVMMSQTKPNENG ---GESFEQLQ------ELFEEMFQGDI--EG----------FSSCSQP------------ -----PTSCSTSSSS------------------YALYCENST--------PSNKRNSS-AM -NYGN--ATLDSSGFDAHF------HNFCVG-T-----------GGKPAKDREGD-ARKRK -DSRRSNR--------------------------------- +---MAGGKWVPPPLSQFHLHIKRFRRRQKVSGSSGNTEPSGYTDCKNISNRRMEEKGNDF +YAVMGLKKECSDSELRNAYKKLALIWHPDRCSASG---NSKFVEEAKKKFQDIQQAYS-- +----VLSDANKRFLYDVGAYESDD--------DENGMGDFLNEMAVMMSQTKPNENG--G +ESFEQLQ------ELFEEMFQGDI--EG---F--SSCSQP----------------PTSC +STSSSS------------------YALYCENST--------PSNKRNSS-AMNYGN--AT +LDSSGFDAHF--------------HNFCVG-T-----------GGKPAKDREGD-A-RKR +KDSRRSNR--------------------------------- >gnl_Mimgu1.0_PACid_17694730 ----MAAD-------------------------------------------------EEKS -SDFYGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASG---NLKYVEEAKNKFQAVQQAY -S------VLSDANKRFLYDVGIYDSE------DDADENGMGDFLNEMVAMMGQSKPNENK ---NESFQELQ------DLFEEIFNNDA--EEV---------FKIPPPH------------ ---FPYQDSCSETRT-----------------------------------ASNKRNAR-EM -GSVN-----FSNIEATPF------EGFCIG-ENVIFGGERIQTRPG---------GGSRR -T--KPKIST-SID-----------------------GLIS +---MAAD----------------------------------------------EEKSSDF +YGVLGLRKECTAAELRVAYKKLAMKWHPDRCSASG---NLKYVEEAKNKFQAVQQAYS-- +----VLSDANKRFLYDVGIYDSED------DADENGMGDFLNEMVAMMGQSKPNENK--N +ESFQELQ------DLFEEIFNNDA--EEV--F--KIPPPH--------------FPYQDS +C---------------------------SETRT--------ASNKRNAR-EMGSVN---- +-FSNIEATPF--------------EGFCIG-ENVIFGGERIQTRPGG----------GSR +RT--KPKIST-SID-----------------------GLIS >gnl_Nelnu1.0_NNU_010544-RA ------------------------------------------------------------ ----------------------MNLLLQKWHPDRCSSSG---NSKFVEDSKKKFQAIQEAY -S------VLSDENKRFLYDVGVYDCDD-----DDDDENGMGEFLGEMATMMSQIKPSENG ---PESLEKLQ------ELFEEMFQRDM--DDG---------FFSPSPQCA---------- ----SFSSSCSSSSS---------------STTYFSYNNNKH---------DNKRNCS-DI -SSMD--DFYTFGTDSIQF------SNFCIG-VE--GGE-DSKVRGGK---------SRRK -SNRRQKVSSSKHDPSCR----------------------- +------------------MNLLLQKWHPDRCSSSG---NSKFVEDSKKKFQAIQEAYS-- +----VLSDENKRFLYDVGVYDCDD-----DDDDENGMGEFLGEMATMMSQIKPSENG--P +ESLEKLQ------ELFEEMFQRDM--DDG--F--FSPSPQ--CA-----------SFSSS +CSSSSS---------------STTYFSYNNNKH---------DNKRNCS-DISSMD--DF +YTFGTDSIQF--------------SNFCIG-VE--GGE-DSKVRGGK----------SRR +KSNRRQKVSSSKHDPSCR----------------------- >gnl_Solly2.3_Solyc03g123560.2.1 ----M----------------------------------------------------EDKS -NDYYAVLGLKKECTDTELRNAYKKLALKWHPDRCSASG---NLKFVDEAKKQFQAIQEAY -S------VLSDANKKFLYDVGVYDSG------DDDDENGMGDFLNEMAAMMSQNKSNENQ --GEETFEELQ------DMFNEMFNSDN--GT----------FSSSSS------------- -----SSSSWTGTPS------------------MCSTTSSTSSSET-FLTFPNKRSSG-EM -KSGS-----SVRGDSCQF------QGFCVG-A-----------GGTSGKCNERE-RSWRK -NSKSGRKH-------------------------------- +---M-------------------------------------------------EDKSNDY +YAVLGLKKECTDTELRNAYKKLALKWHPDRCSASG---NLKFVDEAKKQFQAIQEAYS-- +----VLSDANKKFLYDVGVYDSGD------DDDENGMGDFLNEMAAMMSQNKSNENQ-GE +ETFEELQ------DMFNEMFNSDN--GT---F--SSSSS-----------------SSSS +WTGTPS------------------MCSTTSSTSSSET-FLTFPNKRSSG-EMKSGS---- +-SVRGDSCQF--------------QGFCVG-A-----------GGTSGKCNERE-R-SWR +KNSKSGRKH-------------------------------- >gnl_Sorbi1.4_PACid_1968370 ----MDAGG-------------------------------------EKFSDAAAAEGGEGG -GDLYAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSS---SVKHMEEAKEKFQEIQGAY -S------VLSDANKRLLYDVGVYDDED-----DEDSMQGMGDFIGEMAQMMSQVRPTR-- ---QESFEELQ------QLFVDMFQSDI--DSG---------FCNGSAK-DQVQGQAKSRT -CSTSPSSSPSPPPP----------------PTIVKEAEVSS------CNGFNKRGSS-AM -DSGK-PPRP--VEGGAGQ------AGFCFG-VS--DTKQTPKPRGPN--------TSRRR -NGRKQKLSS-KHDVSSEDETAGS----------------- +---MDAGGE----------------------------------KFSDAAAAEGGEGGGDL +YAVLGLKKECSDADLKVAYRKLAKKWHPDKCSSSS---SVKHMEEAKEKFQEIQGAYS-- +----VLSDANKRLLYDVGVYDDED-----DEDSMQGMGDFIGEMAQMMSQVRPTR----Q +ESFEELQ------QLFVDMFQSDI--DSG--F--CNGSAK-DQVQGQAKSRTCSTSPSSS +PSPPPP----------------PTIVKEAEVSS------CNGFNKRGSS-AMDSGK-PPR +P--VEGGAGQ--------------AGFCFG-VS--DTKQTPKPRGPN--------T-SRR +RNGRKQKLSS-KHDVSSEDETAGS----------------- >gnl_Thepa2.0_Tp3g12470 ----MASNN-----------------------------------------------SEKGN -DDLYGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAY -S------VLSDSNKRFLYDVGAYNS-------DDEDQNGMGDFLNEMAAMMNQSKPSENN --SGDSFEQLQ------DLFNEMFQGDA--AA----------FSSSSS------------- -------SSCSASTF------------------TSSCSFVFD--------TNSQRSPF-ET -SSMG---TNDLFGFDHSA------HTFSLG-VE--HQQDFKKGKN----------SGGRR -NRRKNNAQSAAHETASSNNYGVPTS--------------- +---MASNN--------------------------------------------SEKGNDDL +YGVLGLKKECTTTELRTAYKKLALRWHPDRCSSMG---TPEFVDEAKKKFQAIQEAYS-- +----VLSDSNKRFLYDVGAYNSDD-------EDQNGMGDFLNEMAAMMNQSKPSENN-SG +DSFEQLQ------DLFNEMFQGDA--AA---F--SSSSS-------------------SS +CSASTF------------------TSSCSFVFD--------TNSQRSPF-ETSSMG---T +NDLFGFDHSA--------------HTFSLG-VE--HQQDFKKGKN----------S-GGR +RNRRKNNAQSAAHETASSNNYGVPTS--------------- >gnl_Theca1.0_Tc06_g010450 ----MANG-------------------------------------------------EEKN -NDFYAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAY -S------VLSDSNKRFLYDVGAYDS--------DDDENGMGDFLNEMAGMMSQTKSNENG ---GESFEELQ------ELFEEMFQADI--DS----------FESTGQ------------- -----STPSCSASSS------------------FGSYGESSS---------SNKRNSS-EM -SSVE-TRLESSSSFDAQF------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGGSRRR -NGRKQKVSS-GHDVTSND-CGISAS--------------- +---MANG----------------------------------------------EEKNNDF +YAVLGLNKECTPTELRTAYKKLALRWHPDRCSASG---NSKFVEEAKKKFQAIQQAYS-- +----VLSDSNKRFLYDVGAYDSDD--------DENGMGDFLNEMAGMMSQTKSNENG--G +ESFEELQ------ELFEEMFQADI--DS---F--ESTGQ-----------------STPS +CSASSS------------------FGSYGESSS---------SNKRNSS-EMSSVE-TRL +ESSSSFDAQF--------------HSFCLG-VE--HRQDIKQHRGARGGMRGAAGG-SRR +RNGRKQKVSS-GHDVTSND-CGISAS--------------- >gnl_Vitvi12X_PACid_17827068 ----MAAG-------------------------------------------------EEKS -NDFYAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAY -S------VLSDANKRFLYDVGAYDS--------DDDENGMGDFLNEMAVMMSQTKSNENG ---KESFEELQ------ELFEDMFQRDV--DA----------FNSASHH------------ -----PMNSFPSSTS------------------TSSYCESSN--------ANNKRNSA-EM -GSGRMMSAGESSAFDAHF------QSFCFG-T-----------GGTPGRFQEGE-RSKRR -NSRRSQR--------------------------------- +---MAAG----------------------------------------------EEKSNDF +YAVLGLKKECTASELRNAYKRLALMWHPDRCSSSG---NSKFVEEAKKKFQAIQEAYS-- +----VLSDANKRFLYDVGAYDSDD--------DENGMGDFLNEMAVMMSQTKSNENG--K +ESFEELQ------ELFEDMFQRDV--DA---F--NSASHH----------------PMNS +FPSSTS------------------TSSYCESSN--------ANNKRNSA-EMGSGRMMSA +GESSAFDAHF--------------QSFCFG-T-----------GGTPGRFQEGE-R-SKR +RNSRRSQR--------------------------------- >gnl_Selmo1.0_PACid_15401289 ----M----------------------------------------------------EKRK -EDPYTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAY -S------VLSDDKKRVLYDSGLYDEG------DDE------------------------- +---M-------------------------------------------------EKRKEDP +YTVLGVQKSSSSSEIRSAYRKLAMKWHPDK--------QHSLEDQAKAKFQGIQEAYS-- +----VLSDDKKRVLYDSGLYDEGD--------DE-------------------------- ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------VS--------------------------- ----------------------------------------- +----------------------------------------- >gnl_Orysa6.0_PACid_16864430 ----MARGGG-----------------------------------G----------GGGAD -ADLYAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAY -S------VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP---- ---AESFEELQ------QLFVDMFQDDI--DAG---------LCQSTP------------- -----PPPSWPSPPA-------------------AANARSPAAAAT-SRKGVNKRCSP-AA -MDMD-----SGLSSLLGI------SGFCFE-AP--WTSQDASTAAGGG-------GGKRR -KQRPPPA---SHNV-------------------------- +---MARGG------------------------------------------GGGGGADADL +YAVLGLSRECTDADLRLAYRKLAMIWHPDRCSVAGGSASAAGVDEAKERFQEIQGAYS-- +----VLSDSNKRFLYDVGVYDGNDGDDDDDEADLSGMGDFLGEMAQMMSQATP------A +ESFEELQ------QLFVDMFQDDI--DAG--L--CQSTP-----------------PPPS +W-PSPP------------------AAANARSPAAAAT-SRKGVNKRCSP-AAMDMD---- +-SGLSSLLGI--------------SGFCFE-AP--WTSQDASTAAGGG-------G-GKR +RKQRPPPA---SHNV-------------------------- >gnl_Sorbi1.4_PACid_1982925 ----MAATSH-----------------------------------CGNIQDQDEEASAPGA -ADLYAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAY -S------VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP---- ---TETFEELQ------QVFVDMFQDDLD-DAG---------FFGGLPT-TGRRAQA--PS -TSLPPSVSSSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-ST -AKRPRPNGSAGLESDLGL------SGFCFM-VS--KEMSKSKERQAV---WASD-DGDRS -TDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS +---MAATSHC--------------------------------GNIQDQDEEASAPGAADL +YAVLGLNRECTDAELRVAYRRLAMIWHPDRCSASG--SSPARMEEAKERFQEIQGAYS-- +----VLSDSNKRLLYDVGVYDSDD-----DEADLSGMGDFLGEMADMMSQATP------T +ETFEELQ------QVFVDMFQDDLD-DAG--F--FGGLPT---TGRRAQAPSTSLPPSVS +SSPLRP----------------TPAAGRSKGPQATPSSSFKGVERRGST-STAKRPRPNG +SAGLESDLGL--------------SGFCFM-VS--KEMSKSKERQAV---WASD-D-GDR +STDGKQRLST-SRDVSGGG-MSRSLQGQSSKNLLQCMASKS >gnl_Medtr3.5_Medtr8g022310.3 ----MANE-------------------------------------------------GNKS -NDFYAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAY -S------VLSDSNKRLMYDVGVYDS--------DDDENVRHLF----------------- ----HTIHELG------TLFCVMFCFFISLR------------GE---------------- ----------KRSNL------------------NLTFSLSH-------------------- +---MANE----------------------------------------------GNKSNDF +YAVLGLNKECSDSELRNAYKKLALKWHPDRCSASG---NVKFVEEAKKKFQAIQEAYS-- +----VLSDSNKRLMYDVGVYDSDD--------DENVRHLF-------------------- +HTIHELG------TLFCVMFCFFISLR-------GE------------------------ +-KRSNL------------------NLTFSLSH---------------------------- ------------------------------------------------------------ ----------------------------------------- +----------------------------------------- >gnl_Nelnu1.0_NNU_000115-RA ----MEVD------------------------------------------------SHRSS -PSYYTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAY -SGGLLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC---- ---EETGEEIQLGGTTGDVSGNVTRAGV--EDGECWWCVVVRWSCSLKE------------ -----------------------------------------------------------EL -KEGQ--------------------MGIISE-SD--DA----------------------- -----------GHDTPSLPHLHGSEL-----ELLGRTGCCN ->contig_7 ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------ENEWSGAEFLNEMAAMMTQNKSNENG ---TGTFEELQ------QLFDEMFQSDI--ES----------FNGCSSS------------ -----SNETCS---------------------------------------NSNKRNSI-ES -SSAN----------------FRPENGNESG-----------------------E-ISGKK -NTRKGKGDX------------------------------- +---MEVDS---------------------------------------------HRSSPSY +YTILGVDQNSSASEIRNAYRKLAMQWHPDKWTKTP-----SLLEKAKSKFQQIQEAYSGG +LLVFMLSDQGKRTLYDVGLYDPDD-----ETNDEVGLRRF--HAGDDISHERC------E +ETGEEIQLGGTTGDVSGNVTRAGV--EDG--ECW------------------WCVVVRWS +C-----------------------------------------SLKEELK-EGQMGI-ISE +SDDAGHDTPSLPHLHGSELELLGRTGCCN------------------------------- +-----------------------------------------
--- a/test-data/3722.faa.aln.tree Thu Sep 06 09:40:44 2018 -0400 +++ b/test-data/3722.faa.aln.tree Tue Jul 20 20:29:00 2021 +0000 @@ -1,1 +1,1 @@ -(((((gnl_Glyma1.01_PACid_16301085:0.016443402,gnl_Glyma1.01_PACid_16301084:0.053278093)0.803:0.023390563,gnl_Glyma1.01_PACid_16301083:0.030298601)0.901:0.027099626,((gnl_Glyma1.01_PACid_16266209:0.056847680,gnl_Glyma1.01_PACid_16266210:0.015624714)0.811:0.025333131,gnl_Glyma1.01_PACid_16266208:0.034488143)0.905:0.035494603)0.999:0.188079149,(gnl_Medtr3.5_Medtr8g022310.2:0.024981315,(gnl_Medtr3.5_Medtr8g022310.3:0.465525159,gnl_Medtr3.5_Medtr8g022310.1:0.036690818)0.074:0.002229085)0.952:0.101287628)1.000:0.225059008,(((((gnl_Orysa6.0_PACid_16843526:0.000000007,gnl_Orysa6.0_PACid_16843528:0.000000007)0.960:0.104692276,(gnl_Bradi1.2_Bradi3g60090.1:0.251215525,gnl_Sorbi1.4_PACid_1968370:0.202676729)0.470:0.035571250)0.964:0.220529391,(gnl_Orysa6.0_PACid_16864430:0.468545028,gnl_Sorbi1.4_PACid_1982925:0.504608123)0.995:0.341396682)0.999:0.333764302,((gnl_Musac1.0_GSMUA_Achr6T31040_001:0.257705603,gnl_Musac1.0_GSMUA_Achr9T18140_001:0.233035596)0.837:0.090223569,(gnl_Musac1.0_GSMUA_Achr8T23700_001:0.288734161,gnl_Musac1.0_GSMUA_AchrUn_randomT02210_001:0.550828541)0.916:0.084755065)0.866:0.093086055)0.999:0.343576670,(((gnl_Mimgu1.0_PACid_17694730:0.627920829,((gnl_Soltu3.4_PGSC0003DMP400016106:0.060397140,(gnl_Soltu3.4_PGSC0003DMP400016105:0.000000007,gnl_Solly2.3_Solyc03g123560.2.1:0.117851013)0.917:0.075604816)0.676:0.104109587,(gnl_Selmo1.0_PACid_15401289:0.393757146,gnl_Nelnu1.0_NNU_000115-RA:1.006137326)0.989:1.057259060)0.804:0.231585972)0.632:0.070827174,(gnl_Nelnu1.0_NNU_010544-RA:0.445330506,(gnl_Ambtr1.0.27_AmTr_v1.0_scaffold00007.329:0.481404311,gnl_Aquco1.0_PACid_18141277:0.569001355)0.869:0.111238919)0.913:0.101469446)0.876:0.061617758,(gnl_Frave2.0_gene05408:0.298252983,gnl_Vitvi12X_PACid_17827068:0.183978617)0.975:0.124539672)0.258:0.016419054)0.666:0.050639012,(((contig_7:0.847311108,gnl_Theca1.0_Tc06_g010450:0.107098111)0.806:0.076702503,((gnl_Arath10_AT3G14200.1:0.118641618,gnl_Thepa2.0_Tp3g12470:0.089890295)1.000:0.506633729,gnl_Carpa1.181_PACid_16420351:0.140839270)0.773:0.074226625)0.858:0.037834597,(gnl_Poptr2.2_PACid_18217800:0.237912037,(gnl_Poptr2.2_PACid_18234651:0.048333265,(gnl_Poptr2.2_PACid_18234649:0.000000007,gnl_Poptr2.2_PACid_18234650:0.000000007)0.962:0.063277271)0.890:0.133521212)0.996:0.168273995)0.846:0.051958868); +((((gnl_Glyma1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plant_tribes_scaffolds.loc Tue Jul 20 20:29:00 2021 +0000 @@ -0,0 +1,3 @@ +## Plant Tribes scaffolds +#Value Name Path Description +22Gv1.1 22Gv1.1 ${__HERE__}/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- a/test-data/tool-data/plant_tribes/scaffolds/README.txt Thu Sep 06 09:40:44 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -For functional tests to work, this directory must contain symlinks to the scaffolds data -installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. -This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plant_tribes_scaffolds.loc.sample Tue Jul 20 20:29:00 2021 +0000 @@ -0,0 +1,4 @@ +## Plant Tribes scaffolds +#Value Name Path Description +#22Gv1.0 22Gv1.0 /plant_tribes/scaffolds/22Gv1.0 22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0) +#22Gv1.1 22Gv1.1 /plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- a/tool_data_table_conf.xml.test Thu Sep 06 09:40:44 2018 -0400 +++ b/tool_data_table_conf.xml.test Tue Jul 20 20:29:00 2021 +0000 @@ -1,6 +1,6 @@ <tables> <table name="plant_tribes_scaffolds" comment_char="#"> <columns>value, name, path, description</columns> - <file path="${__HERE__}/plant_tribes_scaffolds.loc" /> + <file path="${__HERE__}/test-data/plant_tribes_scaffolds.loc" /> </table> </tables>