Generate an amino acid alignment with phylogenetic tree and detected peptides overlay.

mapper.pl

#!/usr/bin/perl

#--------------------------------------------------------------#
# Author:      Daniel Patrick Smith                            #
# Version:     1.0 / April 21st, 2010                          #
# Affiliation: Giovannoni Laboratory, Oregon State University  #
# Copyright:   GNU General Public License v3                   #
# Please Cite: Sowell et al, ISME (2009) 3, 93-105             #
#--------------------------------------------------------------#

use strict;
use warnings;

use PostScript::Simple;


# Change the following input data as needed:
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

# The amino acid sequence alignment. Names must not contain '(', ')', ':', ' ', or ','. Names must contain at least one non-numerical character.
our %proteins = qw(
	M_extorquens_moxF                ----MSRFVTSVSALAMLALAPAAL---SSGAYANDKLVELSKSDDNWVMPGKNYDSNNFSDLKQINKGNVKQLRPAWTFSTGLLNGHEGAPLVVDGKMYIHTSFPNNTFALGLDDPGTILWQDK-----PKQNPAARAVACCDLVNRGLAYWPGDGKTPALILKTQLDGNVAALNAETGETVWKVENSDIKVGSTLTIAPYVVKDKVIIGSSGAELGVRGYLTAYDVKTGEQVWRAYATGPDKDLLLASDFNI----KNPHY-----------------------------GQKGLGTGTW-----EGDAWKIGGGTNWGWYAYDPGTNLIYFGTGNPAPWNETMRPGDNKWTMTIFGRDADTGEAKFGYQKTPHDEWDYAGVNVMMLSEQK---DKDGKARKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKSVDLKT-----GQPVRDPEYGTRM---DHLAKDICPSAMGYHNQGHDSYDPKRELFFMGINHICMDWEPFMLPYRAGQFFVGATLNMYPG----PKGDRQNYEGLGQIKAYNAITGDYKWEKMERFAVWGGTMATAGDLVFYGTLDGYLKARDSDT-GDLLWKFKIPSGAIGYPMTYTHKGTQYVAIYYGVGGWPGVGLVFDLADPTAGLGAVGAFKKLANYTQM--GGGVVVFSLDGKGPYDDPNVGEWKSAAK-
	M_extorquens_putMdhLarge         -----MRAVHLLALGAGLAAASPAL--------ANESVLKGVANPAEQVLQTVDYANTRYSKLDQINASNVKNLQVAWTFSTGVLRGHEGSPLVVGNIMYVHTPFPNIVYALDLDQGAKIVWKYE-----PKQDPSVIPVMCCDTVNRGLAY--ADGA----ILLHQADTTLVSLDAKSGKVNWSVKNGDPSKGETNTATVLPVKDKVIVGISGGEFGVQCHVTAYDLKSGKKVWRGYSIGPDDQLIVDPEKTT----SLGKP-----------------------------IAKDSSLKTW-----EGDQWKTGGGCTWGWFSYDPKLDLMYYGSGNPSTWNPKQRPGDNKWSMTIWARNPDTGMAKWVYQMTPHDEWDFDGINEMILTDQ----KFDGKDRPLLTHFDRNGFGYTLDRATGEVLVAEKFDPVVNWATKVDLDKGSKTYGRPLVVSKYSTEQNGEDVNSKGICPAALGTKDQQPAAFSPKTGLFYVPTNHVCMDYEPFRVTYTPGQPYVGATLSMYPA----PGSH----GGMGNFIAWDNLQGKIKWSNPEQFSAWGGALATSGDVLFYGTLEGFLKAVDSKT-GKELYKFKTPSGIIGNVMTYEHKGKQHVAVLSGVGGWAGIGLAAGLTDPNAGLGAVGGYAALSSYTNL--GGQLTVFSLPNN-----------------
	M_methylotrophus_MdhLarge        --------------------------------MADADLDKQVNTAGAWPIATGGYYSQHNSPLAQINKSNVKNVKAAWSFSTGVLNGHEGAPLVIGDMMYVHSAFPNNTYALNLNDPGKIVWQHK-----PKQDASTKAVMCCDVVDRGLAY--GAGQ----IVKKQANGHLLALDAKTGKINWEVEVCDPKVGSTLTQAPFVAKDTVLMGCSGAELGVRGAVNAFDLKTGELKWRAFATGSDDSVRLAKDFNS----ANPHY-----------------------------GQFGLGTKTW-----EGDAWKIGGGTNWGWYAYDPKLNLFYYGSGNPAPWNETMRPGDNKWTMTIWGRDLDTGMAKWGYQKTPHDEWDFAGVNQMVLTDQ----PVNGKMTPLLSHIDRNGILYTLNRENGNLIVAEKVDPAVNVFKKVDLKT-----GTPVRDPEFATRM---DHKGTNICPSAMGFHNQGVDSYDPESRTLYAGLNHICMDWEPFMLPYRAGQFFVGATLAMYPG----PNGP--TKKEMGQIRAFDLTTGKAKWTKWEKFAAWGGTLYTKGGLVWYATLDGYLKALDNKD-GKELWNFKMPSGGIGSPMTYSFKGKQYIGSMYGVGGWPGVGLVFDLTDPSAGLGAVGAFRELQNHTQM--GGGLMVFSL--------------------
	M_organophilum_MdhLarge          ----MSRFVTSVSALAMLALAPAAL---SSVAYANDKLVELSKSDDNWVMPGKNYDSNNYSELKQVNKSNVKQLRPAWTFSTGLLNGHEGAPLVVDGKMYVHTSFPNNTFALDLDDPGHILWQDK-----PKQNPAARAVACCDLVNRGLAYWPGDGKTPALILKTQLDRHVVALNAETGETVWKVENSDIKVGSTLTIAPYVVKDKVIIGSSGAELGVRGYLTAYDVKTGGQVWRAYATGPDKDLLLADDFNV----KNAHY-----------------------------GQKGLGTATW-----EGDAWKIGGGTNWGWYAYDPGTNLIYFGTGNPAPWNETMRPGDNKWTMTIFGRDADTGEAKFGYQKTPHDEWDYAGVNVMMPSEQK---DKDGKTRKLLTHPDRNGIVYTLDRTDGALVSANKLDDTVNVFKTVDLKT-----GQPVRDPEYGTRM---DHLAKDVCPSAMGYHNQGHDSYDPKRELFFMGINHICMDWEPFMLPYRAGQFFVGATLNMYPG----PKGDRQNYEGLGQIKAYNAITGSYKWEKMERFAVWGGTLATAGDLVFYGTLDGYLKARDSDT-GDLLWKFKIPSGAIGYPMTYTHKGTQYVAIYYGVGGWPGVGLVFDLADPTAGLGAVGAFKKLANYTQQ--GGGVIVFSLDGKGPYDDPNVGEWKSASK-
	M_nodulans_MxaF                  MLGKIVVRCRTGVSVAALAALLPLA---GPSALANDKLVELSKSDGNWVMPGKNYDSDNYSKLKQINAENVKNLKVSWQFSTGLLNGHEGAPLVVDGTMYVHTSFPNNTFALGLDDPGKILWQDK-----PKQNPAARSVACCDLVNRGLAYWPGDGKTPSLILKTLLDGHVVALNAQTGETVWKIENSDIRVGSTLTIAPYVVKDKVIIGSSGAELGVRGYLTAYDVRTGEQKWRAYATGPDSDLLLAKDFNI----HNAHY-----------------------------GQKGLGTSTW-----EGDAWKIGGGTNWGWYAYDPGTNLIYFGTGNPAPWNETMRPGDNKWTMTIFARDVDTGEAKFGYQKTPHDEWDYAGVNVMMLSTQK---DRSGKERKLLTHPDRNGIVYTLDRTNGDLISAHKIDDTVNVFKTVDLKS-----GLPVRDPEYGTRM---DHLAKDICPSAMGYHNQGHDSYDPERKLFYMGINHICMDWEPFMLPYRAGQFFVGATLNMYPG----PKGDRQNAEGLGQIKAYDAITGKFKWEKMERFAVWGGTLATAGNVVFYGTLDGFIKARHSDT-GELLWKAKLPSGAIGYPVTYTHKGTQYVAIYYGVGGWPGVGLVFDLQDPTAGLGAVGAFKKLANYTQM--GGGVTVFSLDGKGPYDDPNTGEYVAAN--
	P_denitrificans_MdhLarge         -MNRNTPKARGASSLAMAVAMGLAV-LTTAPATANDQLVELAKDPANWVMTGRDYNAQNYSEMTDINKENVKQLRPAWSFSTGVLHGHEGTPLVVGDRMFIHTPFPNTTFALDLNEPGKILWQNK-----PKQNPTARTVACCDVVNRGLAYWPGDDQVKPLIFRTQLDGHIVAMDAETGETRWIMENSDIKVGSTLTIAPYVIKDLVLVGSSGAELGVRGYVTAYDVKSGEMRWRAFATGPDEELLLAEDFNA----PNPHY-----------------------------GQKNLGLETW-----EGDAWKIGGGTNWGWYAYDPEVDLFYYGSGNPAPWNETMRPGDNKWTMAIWGREATTGEAKFAYQKTPHDEWDYAGVNVMMLSEQE---DKQGQMRKLLTHPDRNGIVYTLDRTNGDLISADKMDDTVNWVKEVQLDT-----GLPVRDPEFGTRM---DHKARDICPSAMGYHNQGHDSYDPERKVFMLGINHICMDWEPFMLPYRAGQFFVGATLTMYPG----PKGDRQNALGLGQIKAYDAISGEMKWEKMERFSVWGGTMATAGGLTFYGTLDGFIKARDSDT-GDLLWKFKLPSGVIGHPMTYKHDGRQYVAIMYGVGGWPGVGLVFDLADPTAGLGSVGAFKRLQEFTQM--GGGVMVFSLDGESPYSDPNVGEYAPGEPT
	M_capsulatus_Bath_MdhLarge       -----MQICKLASGCGGSMLAMAAVLA-AQSTHANSELDRLSKDDRNWVMQTKDYSATHFSRLTEINSHNVKNLKVAWTLSTGTLHGHEGAPLVVDGIMYIHTPFPNNVYAVDLNDTRKMLWQYK-----PKQNPAARAVACCDVVNRGLAYVPAGEHGPAKIFLNQLDGHIVALNAKTGEEIWKMENSDIAMGSTLTGAPFVVKDKVLVGSAGAELGVRGYVTAYNIKDGKQEWRAYATGPDEDLLLDKDFNK----DNPHY-----------------------------GQFGLGLSTW-----EGDAWKIGGGTNWGWYAYDPKLDMIYYGSGNPAPWNETMRPGDNKWTMTIWGRDADTGRAKFGYQKTPHDEWDYAGVNYMGLSEQ----EVDGKLTPLLTHPDRNGLVYTLNRETGALVNAFKIDDTVNWVKKVDLKT-----GLPIRDPEYSTRM---DHNAKGICPSAMGYHNQGIESYDPDKKLFFMGVNHICMDWEPFMLPYRAGQFFVGATLNMYPG----PKGM------LGQVKAMNAVTGKMEWEVPEKFAVWGGTLATAGDLVFYGTLDGFIKARDTRT-GELKWQFQLPSGVIGHPITYQHNGKQYIAIYSGVGGWPGVGLVFDLKDPTAGLGAVGAFRELAHYTQM--GGSVFVFSL--------------------
	M_capsulatus_Bath_putMdhLarge    -MKKPVKSWLIASSIASLLAVPGVS-------FANAEVEALTKDPKNFATWGGNYAGTRYSTLDQINFKNAKHLQPVWTFSTGMLRGHEGGPLVVNDVIYIHTGYPHKVYALDQATQ-SVIWEYVYAPDKGTDQSQVISVMCCDVVNRGLAY--GDGK----IFLAQGDATLVALDAKTGKIVWKVKNGDPKTGMTATNAPLVVKDKVLTGISGGEFGVRGFLAAYNIKDGSLVWKKYSMGPDDEVGLDPEHTMTWTDGKMAP-----------------------------VGKDSSLKTW-----QGDQWKIGGGTTWGWYSYDPDLNLVYYGSGNPSTWNPVQRPGDNKWSMTIWARDVDTGEAKWVYQMTPHDEWDYDGINEMMLIDQEMTAKDGSKHSKLLTHFDRNGFGYTLDRVTGELLVAEKFDKAVNWATHVDMKT-----GRPQVNPKYSTQHGGQDVDTKGICPSAMGAKNEPPVTYSPRTKLIYIPGNHTCMNYEPFEVEYTAGQPYVGATLNIFPARANVKTGEKESSNHMGSFTAWDPTTGTIAWQFDEPFSLWSGMVSTAGDIVIYGTLEGYLKVRDAKT-GEELYRFKTPSGIIGNVSTWTYNGKQYIGVLSGIGGWAGVGMAAGLEGDTEGLGAVGAYKGLSSHTKL--GGVFTVFALP-------------------
	S_meliloti_1021_MdhLarge         -------MKRLLTMLAIMSIGGGAQ-----VAFANDELQKLIDDPNQWAIQTGDYANLRYSKLDQINKDNVGKLQVAWTFSTGVLRGHEGSPLVIGDLMYVHTPFPNTVYALDLSKDGQIVWKYE-----PKQDPNVIPVMCCDTVNRGVAY--ADNK----IFLHQADTTVVALDAKTGKVIWSVKNGDATKGETNTATVMPVKDKILVGISGGEFGVRGHVTAYSMADGKVLWRGYSMGPDSDTLIDPEKTT----HLGKP-----------------------------VGKDSGLTTW-----EGDQWKIGGGTTWGWYSYDPEENLVYYGTGNPSTWNPTQRPGDNRWSMTIFARDVDTGMAKWLYQMTPHDEWDYDGVNEMILTEQ----QIDGKDRKLLTHFDRNGFGYTMDRVTGELLVAEKYDPTVNWATEVVMDPKSDKYGRPQVVAQYSTEQNGEDTNTTGVCPAALGTKDQQPAAYSPKTELFYVPTNHVCMDYEPFRVSYTAGQPYVGATLSMYPP----KDSH----GGMGNFIAWDNKEGKIKWSLPEPFSVWSGALATAGDVVFYGTLEGYLKAVDAAT-GKELYRFKTPSGVIGNVMTYAREGKQYVAVLSGVGGWAGIGLAAGLTNPTEGLGAVGGYSALSNYTAL--GGTLTVFKLPE------------------
	S_meliloti_MdhLarge              -------MNRLLTMLAIMSIGGGAQ-----VAFANDELQKLIDDPNQWAIQTGDYANLRYSKLDQINKDNVGKLQVAWTFSTGVLRGHEGSPLVIGDLMYVHTPFPNTVYALDLSKDGQIVWKYE-----PKQDPNVIPVMCCDTVNRGVAY--ADNK----IFLHQADTTVVALDAKTGKVIWSVKNGDATKGETNTATVMPVKDKILVGISGGEFGVRGHVTAYSMADGKVLWRGYSMGPDSDTLIDPEKTT----HLGKP-----------------------------VGKDSGLTTW-----EGDQWKIGGGTTWGWYSYDPEENLVYYGTGNPSTWNPTQRPGDNRWSMTIFARDVDTGMAKWLYQMTPHDEWDYDGVNEMILTGQ----HIDGKDRKLLTHFDRNGFGYTMDRVTGELLVAEKYDPTVNWATEVVMDPKSDKYGRPQVVAQYSTEQNGEDTNTTGVCPAALGTKDQQPAAYSPKTELFYVPTNHVCMDYEPFRVSYTAGQPYVGATLSMYPP----KDSH----GGMGNFIACDNKEGKIKWSLPEPFSVWSGALATAGDVVFYGTLEGYLKAVDAAT-GKELYRFKTPSGVIGNVMTYAREGKQYVAVLSGVGGWAGIGLAAGLTNPTEGLGAVGGYSDLSNYNAL--GGTLTEFKLPE------------------
	B_japonicum_USDA_110_MdhLarge    -----MRKVLLATYLGSAAALAVGS------ASANDELIKMSQNPKDWVMPAGDYANTRYSKLNQINAQNVGKLQVAWTFSTGVLRGHEGGPLIIGNMMYVHTPFPNKVYAIDLSNENKIVWKYE-----PKQDPNVIPVMCCDTVNRGLSY--GDGK----IILHQADTNLVALDAKTGQVAWSATNGDPSKGQTGTSAALVVKDKVLVGISGGEFGVQCHVTAYDLKSGKQVWRAFSEGPDDQIKVDPAKTT----SLGKP-----------------------------VGADSSLKTW-----QGDQWKIGGGCTWGWMSYDPALNLVYYGSGNPSTWNPKQRPGDNKWSMTIFARDADTGMAKWVYQMTPHDEWDYDGVNEMILSDQ----QINGQARKLLTHFDRNGLGYTMDRESGELLVAEKYDPKVNWTSGVDMDKNSPTYGRPKVLDAASTDKAGEDHNVKGICPAALGTKDEQPAAYSPDTQLFYVPTNHVCMDYEPFKVSYTAGQPYVGATLSMYP-----PQGE----SHMGNFIAWDGKTGKIVWSNKEQFSVWSGALATAGGVVFYGTLEGYLKAVDAKS-GKELYKFKTPSGIIGNVTTYENGGKQYVAVLSGVGGWAGIGLAAGLTDPTAGLGAVGGYAALSNYTAL--GGTLTVFSLPAN-----------------
	HTCC2181_putMdhLarge             -MEINMQLNKIKLALGFAAAATMAM---PMVASAAADQEKAMSNANNWAHPRGQHDNQAYSKLTQLNKGNVKNLKAAWTFATGVNRGHEGSPLVIGNMMYVHTAFPNNVYALDLNNDQKIVWSYF-----PKQDPSVQAVLCCDNVNRGLGF--GDGK----IFLQQNDGMLVALDAKTGAKVWDASNVDPKVGATNTNAPHVIKDKVLTGCSGAEFGVRCFMAAYNIADGSLAWKAMSTGPDSEVLIGADFNK----ENPLYSALSVYEDVNGGNKQGGSFKKIPTDQLQGGVADLGVKTWLKPQAVKDGWQHGGGSVWGWWPYDAKTNLVYYGTGNPSVWNPDVRPGDNKWSMTVFARDLDTGMARWGMQMTPHDEWDYDGINEVILFDK------GGK--TYAWHHDRNGFAYTWTAAEGTLVAAEKVHPFVNWATDVDLKS-----GVPNKLAEHSTHQ---DYNTKGTCPAALGTKDQQPAAYSPKTGLIYSPLNHVCMTYEPVESKYVAGQPWVGATLTMFAG----PDGV------MGGFAAYDPMTNKKVWYNKEKFSAWGGAMTTASDLVFYGTLDRWFKALDAKS-GKELWKFQVGSGVIGNAFTYAHKGKQHVGVLSGIGGWAGVAMNLGLTNDTDALGAAGGYKELTKYNAAPGGGGLTVFSL--------------------
	M_flagellatus_KT_Mfla_2314       -----MEMSKIKLALGVAFGMAMAV---PMVASAAADQEAAMKDPNNWVHPRGQHNNQGYSTLNQINKSNVKNVKAAWQFATGVNRGHEGSPVVIGNMMYVHTAFPNNVYALDLNDNQKIVWAYF-----PKQDPSVQAVLCCDNVSRGLGY--GDGK----IFLQQNDGVLVALDAKTGAKVWDVKVNDPKVGATNTNAPHVIKDKVLTGCSGAEFGVRCFLVAYNIKDGSQVWKAYSTGPDSEVLIGKDFNK----DNPHYSALSVYEDINGGNKEGGSFKALPKEKLKFPETDLGVKTWLKPQAVKDGWQHGGGSTWGWWPYDHRTNLVYYGTGNPSVWNPDVRPGDNKWSMTIFARDVDTGIAKWGYQMTPHDEWDYDGINEVILFDK------GGK--TYAWHHDRNGFAYTFDAHTGSIIAAEKVHPFVNWATHVDKAT-----GIPHKDGKYSTHQ---DYNTKGICPAALGTKDQQPAAYSPRTGLVYSPLNHVCMTYEPVESKYIAGQPWVGATLTMFAG----PDGV------MGGFAAYDPMTNKAKWYNKEKFSAWGGALATASDLVFYGTLDRWFKALDAQT-GKELWKFQVGSGVIGNAFTYSHKGKQYVGVLSGIGGWAGVAMNLGLENETDALGAAGGYKELTKYNAAPGGGALNVFSL--------------------
	M_flagellatus_KT_Mfla_0344       -----MKAKHLKIALGASLIGLASI-----PGFAATDLEKLMQDDNQWATQRKDYANTGYSKLSQINQSNIKNLKAAWTFATGVNRGHEGAPLVVDDTLYFTTAFPNNVYALDLNNEEKIKWSYF-----PKQDPSVQALLCCDNVTRGLAY--GDGK----IFLQQNDGQLVALDAKTGAKVWEVGVVDVKQGATTTNAPHVFKDKVITGCSGGEYGVRCYLTAYNIKDGSIAWRAYATGPDSDVLIGKDFNK----DNPHYSALSVYEDINGGNQEGGSFKALPKEKLKFPETDLGVKTWLKPQAAKNGWEHGGGGTWGWYSYDPALNLVYYATGNPSVWNPDVRPGDNKWSMTIFARDLDTGLAKWGYQLTPHDEWDYDAVNETILWDA------DGK--KLATHFDRNGFGYTLDRQTGKLLVAEKMHPFVNWATGIDLTT-----GTPIKDPKYATHQ---DVQISGICPAALGVKDQQPAAYSPKTKLFYVPLNHVCMDYEPVEVKYVAGQPWVGATLSMYPG----PDGV------MGGFMAWDGLKGKQVWYKKEKFSVWSGALATATDIVFYGTLDRWFKAVDAKS-GKELWKFRVGSGVVGNPITYTHKGKQYVALLSGIGGWAGVAMNLGLTNDNEGLGAAGGYKELKEWNAAPGGGALNVFSL--------------------
	M_flagellatus_KT_Mfla_1717       -----MRISPFLIVVSLNLVSAVSS--------AADPLLPLLQDDKQWVSPRKDYYNQGYSRLSQINHRNVANLKLAWSFSTGVQRGHEGAPLVVGNVMYVHTAFPNNVYALDLDHDQKILWAYF-----PKQTSDIEAILCCDSVSRGLAY--GDGK----ILLQQNNGILLALDARDGRKVWEVQVNDPRMGATNTNAPYVFRDKVLTGCSGGEFGVRCFLAAYALQDGRLQWKAYSTGPDSEVLIGPGFNA----ENPHYSALSTYEDVNGGNREGGSFRALPKERLKFPETELGVKTWLKPQAAANGWQHGGGPVWGWFSYDPKLNLVYYGTGNPSVWNPDIRPGDNKWAMTLFARDLDTGMARWGYQLTPHDEWDYDSVNELILWDQ-------GS-RKLATHFDRNGFAYTLDRQNGKLLAAEKMHPFVNWATGIDLQT-----GIPLKDGRYATHE---DQETSAICPSAIGVKNIQPAAYSPQNGWFYVPMNHLCMTYEAVEAKYVAGQPWAGASLSMYPG----PDGD------MGAFMAWDALKHKPVWYTREKYPVWSGALATAGQLAFYGTLDRWFKALDARN-GKELWRFQVGSGIVGNPMTYQHAGKQYVAVFSGIGGWAGVALNQGLTGDSDGAGTAGAFRGLSQENAAPGSGALNVFAL--------------------
	M_flagellatus_KT_MxaF            ---MKGRVSHVGISAAVSSLLVLAT---VQGAQANQEVLNLQKNADNWALQTGNYTGQHNSTLSQINKSNVKNLKAAWSFSTGVLHGHEGAPLVIGDMMYVHSAFPNNTFAINLNDPGVIAWQHK-----PKQIASVKAVACCDIVNRGLAY--GDGK----IVKTQLDGRLVALDAKSGKIVWEIEVCDPKVGATLTQAPFVAKNSVLVGCSGAELGVRGAVNSFNLKTGELQWRAFATGPDEEVRLAKNFNS----DNPHY-----------------------------GQFGLGLKTW-----EGDAWKIGGGTNWGWYAYDPKLNLFYYGSGNPAPWNETMRPGDNKWTMTIWARDLDTGEAKWGYQKTPHDEWDFAGVNQMILSDH----KVDGKVTPLLTHIDRNGIMYTLNRDNGNLIQAAKVDPAVNVFKKVDLKT-----GTPVRDPEFSTRM---DHKSTNVCPSAMGFHNQGLDALDLDEPIVYAGLNHICMDWEPFMLPYRAGQFFVGATLAMYPG----PSGP--TKKEMGQVRAMDIVTGKYKWTKWEKFAVWGGTLATKGGLVVYNTLDGYIKALDKDN-GKDLWKFKMPSGGIGAPMTYQFKGKQYIGSMYGVGGWPGVGLVFDLTDPSAGLGAVGAFKELQNHTQM--GGGLMVFSL--------------------
	P_denitrificans_xoxF             -------MKNLMNGACLALLMSGTA------ALANEQRAGRDRQAPQWAIQMGDYANTRYSTLDQINKDNVKDLRVAWTFSTGVLRGHEGSPLVIGDVMYVHTPFPNRVFALDLNDNGKILWRYE-----PQQDPNVIAVMSCDTVYRGLSY--ADGM----ILLGQADTTVVALDATSGEVKWSTKIGDPGIGETLTATVVPVKDKVLVGISGGEYGVRGRMTALNLTDGSEAWKAWSTGPDEELLVDPETTT----HLGKP-----------------------------IGADSSLNSW-----EGDQWQIGGGTIWGWFSYDPDLNLVYYGTGNPSTWNPSQRPGDNKWSMTIMARDADTGMAKWFYQMTPHDEWDYDGVNEMILTNQ----TVDGQERKLLTHFDRNGLAYTMDRETGELLVAEKYDPVVNWTTGVDMDPNSETYGRPAVVAEYSTAQNGEDENTTGVCPAALGTKDQQPAAFSPKTNLFYVPTNHVCMDYEPFRVAYTAGQPYVGATLSMYPA----PNSH----GGMGNFIAWHNTTGEIKWSVPEQFSVWSGALATAGDVVFYGTLEGYLKPVDAQT-GEELYKFKTPSGIIGNVMTYEHGGKQYVGILSGVGGWAGIGLAAGLTNPNDGLGAVGGYASLSQYTEL--GGQLTVFELPG------------------
	B_fungorum_GluDH                 -----MNLRTTVLGLAILASAALSS----FVAQADSQLDGLMKNPSNWAAQAGDYANHRYSPLKQINENNVGKLQVAWTMSTGVLRGHEGAPLVIGDTMYIHSPFPNKVIAINLKDQ-TFIWQYL-----PKQDDQVVSVMCCDTVNRGLAY--GDGK----IFLQQADTKLVALNAKTGDVVWTAQNGNPKAGETNTNAPHVFGDKVLTGISGGEFGVRGRLIAYDIKTGKPAWTAYSTGPDKDMLIDPDKTTTYADGKMVP-----------------------------VGADSSLKSW-----KGDQWKLGGGTTWGWYAWDPKLNLVYYGTGNPGTWNPTQRPGDNKWSMSIFARDLNTGQARWVYQMTPHDEWDYDGVNEMILSDL----SIDGKKVPAIVHFDRNGFGYTLNRETGQLLVAQKFDPAVNWADHVDMKS-----GKPIRNAAYSTQAAGSDHNVKGICPAALGSKDQQPAAYDPGSSLFLVPTNHVCMDYEPFDVDYVSGQPYVGATLSMYPG----PNDN----NSMGNFIAWDASKGKIVWSKPERFSVWSGVLATAGGVAFYGTLEGYIKAVRIKD-GKELWRFKTPSGIIGNVFTYEYQGKQFIGVYSGIGGWAGIGMAAGLEKSTEGLGAVGGYRELAKYTAL--GGTLFVFAIPGGNS---------------
	H_methylovorum_mxaF              MGMKKVVSTPMLMSASCMAIAVALQVGVASSAYANDKLIELSKSNENWVMPGKNYDSNNYSESTQVNAENVKQLKHAWSFSTGELHGHEGAPLVIGDMMYVHSSFPNKTFALNLNDPGHILWQHS-----PKQDPAARSVACCDLVNRGLAYWPGDDKTPALVIKTQLDGHLVALNAKTGEEFWKVENGDIKVGQTLTQAPYVVHDLAIVGSSGAELGVRGHVTAYNVKTGEQAWRYYATGPDEEIGLADDFNS----ANPHY-----------------------------GQKGLGTATW-----EGDAWKIGGGTNWGWYAYDPQANLIYYGSGNPAPWNETMRPGDNKWTMTITARDADTGKMKFGYQKTPHDEWDFAGVNVIMLSEQT---DKEGKKRKLLTHPDRNGIVYTLDRENGDLISADKLDDTVNVFKHVDLKS-----GLPVRDPEFGTRM---DHKGTEICPSAMGYHNQGHDSYDPTKQLFFMGINHICMDWEPFMLPYRAGQFFVGATLWMYPG----PKGDRQNYLGLGQIKAYNAITNTYKWEHMERFSVWGGTLATAGNLVFYGTLDGFLKARNSDT-GELLWKHKLPSGVIGYPMTYEHKGVQYIAVMSGVGGWPGVGLVFDLQDPTAGLGAVGAFKNLQRYTQM--GGSLEVFSLDGKNPYDDVNVANWTKGCI-
	R_sphaeroides_GluDH              -------MKMLKRGLAATLLLSSAP------VYANDSVMQAIGDSTQWAIQTGDYANTRYSELDQINRENVGKLQVAWTFSTGVLRGHEGSPLVIDGIMYVHTPFPNNVYALDLNNEGRILWRYE-----PQQNPDVVGVMCCDTVNRGVAY--ADGM----IFLHQADTTIVALDAKSGEVKWSVVNGDPTKGETNTATVLPVKDKILVGISGGEFGVRGHLTAYDMQTGEQVWRAFSTGPDEEMLVDPEQTT----HLGKP-----------------------------IGPNSSLESW-----EGDQWQIGGGTTWGWYSYDPDLNLVYYGTGNPSTWNPSQRPGDNKWSMTIMARDVDTGMAKWFYQKTPHDEWDYDGVNENILVDQ----EIDGQMRKLLVNLDRNGFGYTLDRETGELLVAEKYDPAVNWATEVVMDPESDQYGRPQVVAEYSTAQNGEDTNTTGVCPAALGSKDQQPAAFSPKTGLFYVPTNHVCMDYEPYRVSYTAGQPYVGATLSMYPA----PDSH----GGMGNFIAWDATKGEIKWSLPEQFSVWSGALATAGDVVFYGTLEGHLKAIDAET-GELLYRFKTPSGVIGNVMTYELNGKQYIGILSGVGGWAGIGLAAGLTNPNEGLGAVGGYAALSDYTEL--GGQLTVFAVPD------------------
	Methylobacillus_sp_SK5_MdhLarge  ---MKGRVTHVGISAAVSSLLVLAT---MQGAQANQDLQNLTKNADNWALQTGNYTGQHNSTLSQINKGNVKNLKAAWSFSTGVLHGHEGAPLVIGDMMYIHSAFPNNTFAVNLNDPGVIAWQHK-----PKQIASVKAVACCDIVNRGLAY--GDGK----IVKTQLDGKLVALDAKSGKVVWEIEVCDPKVGATLTQAPFIVKNTVLVGCSGAELGVRGAVNSFNLKTGELQWRAFATGPDEEVRLAKNFNS----DNPHY-----------------------------GQFGLGLKTW-----EGDAWKIGGGTNWGWYAYDPKLNLFYYGSGNPAPWNETMRPGDNKWTMTIWARDLDTGEAKWGYQKTPHDEWDFAGVNQMILSDH----KVDGKVTPLLTHIDRNGIMYTLNRDNGNLVQAAKVDPAVNVFKKVDLKT-----GTPVRDPEFSTRM---DHKSTNVCPSAMGFHNQGLDALDLDEPIVYAGLNHICMDWEPFMLPYRAGQFFVGATLAMYPG----PSGP--TKKEMGQVRAMDIVTGKYKWTKWEKFAVWGGTLATKGGLVAYNTLDGYIKALDKDN-GKELWKFKMPSGGIGAPMTYQFKGKQYIGSMYGVGGWPGVGLVFDLTDPSAGLGAVGAFKELQNHTQM--GGGLMVFSL--------------------
	M_petroleiphilum_PM1_Mpe_A3393   MKVSKHSGWRLMRPLGLALLAIPAV------VQANADVEKNIANSKNWAMQAGDMFNQRYSKLDQINKGNVGKMQVAWTFSTGVLRGHEGSPLVIDGTMYLHSPFPNKVFAIDLNTQ-KILWKYE-----PKQDPAVIPQMCCDTVNRGLAY--AEGK----VILQQADSNLVALDAKSGKVVWSVKNGDPKLGAVNTNAPHVFKDKVITGISGGEWGVRGFIAAYNLKDGKPAWKGYSVGPDAEMLIDPAKTTTWIDGKVAP-----------------------------VGADSSLKTW-----KGDQWKIGGGTTWGWYSYDKALNAMYYGTGNPSTWNPSQRPGDNKWSMSIWSRDVDTGKVNWVYQMTPFDEWDFDGINEMILADI----NVKGKPTKALVHFDRNGFAYTMDRTNGALLVAEKYDPKVNWATHVDMKT-----GRPQVVKQYSTAQNGPDVNTKGICPAALGSKDQQPASFDPNTKLFYVPTNHVCMDYEPFKVEYTAGQPYVGATLSMFPA----PGSH----GGMGNYITWDAGTGKIVQSKAEKFSVWSGSLNTAGGLSCYGTLEGYFKCVDAKDISKELFKFKTPSGIIGNVFTYEHKGKQYMGVFSGIGGWAGIGMAAGLEKDQDGLGAVGGYKELNQYTEL--GGSLTVFALPN------------------
	);

# The list of peptides that are to be highlighted.
our @peptides = unique(qw(
	TNLVYYGTGNPSVWNPDVRPGDNK AMSNSANWAHPR VITGCSGAEFGVR LTQVNKGNVK EAAHSTHQDYNTK
	GLGFGNGKIFLQQNDGNLVALNAK QDPSVQAVLCCDNVNR NGFAYTWVASNGTLVSAEK KIPTDQLQGGVADLGVK
	VGATNTNAPHVIKDK VLTGCSGAEFGVR AAWTISTGVNR GQHDNQAYSK RIPNDQLQAPVADLGIK
	WGMQMTPHDEWDYDGINEVILFDKGGK IFLQQNDGNLVALNAK VGATNTNAPHVINDK LTQLNKGNVK
	DQQPAAYSPK VVWSYFPKQDPSVQAVLCCDNVNR DGWQHGGGSTWGWWPYDAK TGLIYSPLNHVCMTYEPVESK
	AAWTLSTGVNR WGMQMTPHDEWDYDGINEVILFDK RIPNDQLQGGVADLGLK DGWQHGGGSVWGWWPYDAK
	VGATNTNAPHVIK LTQINKGNVK VWSTLNTDPK ELTKYNAAPGGGALTVFAL TWLKPQAVK VVWSYFPK
	));

# The phylogenetic tree in nexus format. Names must be identical to those in the alignment.
# Make sure the string ends in "):0.0;", as in the example below.
our $tree = "((((M_capsulatus_Bath_MdhLarge:0.25935233153341924472,((H_methylovorum_mxaF:0.20878168596712515237,(M_nodulans_MxaF:0.12190741832194466887,(M_extorquens_moxF:0.02274678088090198447,M_organophilum_MdhLarge:0.02307171873930398062):0.06011530645090353009):0.08366283963156732895):0.06995643960127288785,P_denitrificans_MdhLarge:0.20442045141664449970):0.12242880488028372310):0.14514292177919754789,((Methylobacillus_sp_SK5_MdhLarge:0.01600304631180017589,M_flagellatus_KT_MxaF:0.01526122172147443765):0.10767993129317506018,M_methylotrophus_MdhLarge:0.14280191029943056780):0.19923880678630695451):0.42551609073153434659,((M_flagellatus_KT_Mfla_1717:0.35231344928419872087,M_flagellatus_KT_Mfla_0344:0.14695574411891779154):0.06730097283858139934,(M_flagellatus_KT_Mfla_2314:0.06839777440088301574,HTCC2181_putMdhLarge:0.14290213930651829433):0.15771954238829591355):0.22366507158804760369):0.19229690543073024722,((M_petroleiphilum_PM1_Mpe_A3393:0.27375376371657816899,B_fungorum_GluDH:0.32568960184059214669):0.07065861624495217708,((M_extorquens_putMdhLarge:0.20052498854951039675,B_japonicum_USDA_110_MdhLarge:0.20384942278865467169):0.06929269248036029616,((R_sphaeroides_GluDH:0.13212536758338755405,P_denitrificans_xoxF:0.18460378179484654426):0.08680998014121153739,(S_meliloti_1021_MdhLarge:0.00000087024666238173,S_meliloti_MdhLarge:0.01447501190371387053):0.11910797865841461773):0.04195425485701579499):0.13380076964851062016):0.02532900152403316091,M_capsulatus_Bath_putMdhLarge:0.44978920877462219563):0.0; ";

# Parameters concerning the size of the .eps formatted output.
our ($height, $width, $buffer, $textsize, $tree_zoom) = (225, 600, 20, 6, 1);

# Output file. Must be EPS. To convert to other formats, use Imagemagick (`convert out.eps out.png`)
# or ghostscript (`gs -sDEVICE=pdfwrite -sOutputFile="out.pdf" -dNOPAUSE -dEPSCrop -f out.eps -c quit`)
our $outfile = "out.eps";


# That's all
#------------------------------------------------------------------------#
# Don't change anything below this line unless you know what you are doing






# Do some quick sanity checks
die ("No input alignment.\n") unless (scalar(keys %proteins));
our $alignment_len = length((values %proteins)[0]);
die ("Error: Zero-length alignment.\n") unless ($alignment_len);
while (my ($id, $seq) = each %proteins) {
	die ("Sequences are not aligned.\n") if (length($seq) != $alignment_len);
	die ("Name '$id' contains invalid characters.\n") if ($id =~ m/[\(\)\:\,]/);
	die ("Sequence names cannot be all numbers ($id).\n") if ($id =~ m/^\d+$/);
	$proteins{$id} = $seq = uc($seq);
	die ("Invalid sequence for '$seq'.\n") unless ($seq =~ m/^[\-ARNDCEQGHILKMFPSTWYV]+$/);
}
if (scalar(@peptides)) {
	foreach my $i (0..$#peptides) {
		my $seq = $peptides[$i] = uc($peptides[$i]);
		die("Invalid peptide '$seq'.\n") unless ($seq =~ m/^[\-ARNDCEQGHILKMFPSTWYV]+$/);
	}
} else {
	print STDERR "Warning: No peptides provided in input. Proceeding...\n";
}


# Find out how often each amino acid occurs at each position
our @consensus = ();
foreach my $p (0..($alignment_len - 1)) {
	my $hash = {};
	   $hash->{substr($_, $p, 1)}++ foreach (values %proteins);
	my $total = sum(values %$hash);
	$hash->{$_} /= $total foreach (keys %$hash);
	push @consensus, $hash;
}


# Digest the tree data into a form we can recurse over
our @nodes = ();
our @members = ();
while ($tree =~ m/(\([^\(\)]+\))/) {
	substr($tree, index($tree, $1), length($1), scalar(@nodes));
	
	my @pair = ();
	my $member_count = 0;
	foreach (split(',', substr($1, 1, -1))) {
		my ($name, $len) = split(':', $_);
		
		push @pair, { 'name' => $name, 'len' => $len };
		if ($name =~ /^(\d+)$/) {
			$member_count += $members[$1];
		} else {
			$member_count++;
			if (!defined($proteins{$name})) {
				die ("Name in tree '$name' not in the alignment.\n");
			}
		}
	}
	
	push @nodes, [@pair];
	push @members, $member_count;
}


# Set up variables to describe our drawing area
my $scalebar_height = 10 + ($textsize * 2);
my $n_leaves = $members[-1];
my $usable_height = $height - (2 * $buffer) - $scalebar_height;
our $rect_height = $usable_height / $n_leaves;
our $rect_halfheight = $rect_height / 2;
our ($rect_x1, $rect_x2) = ($width * .45, $width - $buffer);
our $rect_width = ($rect_x2 - $rect_x1) + 1;
our @names_ypos = map($buffer + $usable_height * $_ / $n_leaves, 0..($n_leaves-1));
our $text_x_adjust = ($textsize * .3);
our $text_y_adjust = -1 * ($textsize * .3);
our $linesize = $textsize / 10;

our $p = new PostScript::Simple(colour => 1, xsize => $width, ysize => $height, units => "pt");
    $p->setfont("Arial", $textsize);
    $p->setlinewidth($linesize);

# Draw the scale bar for the genes
my $scale_ypos = $height - $buffer - $scalebar_height + 2;
my $interval = int(($alignment_len / $rect_width) * 50); # Number of genes per 40 pixels
my $base     = 10 ** (length($interval) - 1);
   $interval = sprintf("%.0i", $interval / $base) * $base;
my $extended_len  = $interval * int($alignment_len / $interval);
   $extended_len += $interval if ($extended_len < $alignment_len);
my $extended_x2   = $rect_x1 + $rect_width * ($extended_len / $alignment_len);
$p->line($rect_x1 - .5 * $linesize,$scale_ypos, $extended_x2 + .5 * $linesize,$scale_ypos);
for (my $i = 0; $i <= $extended_len; $i += $interval) {
	my $x = $rect_x1 + $rect_width * ($i / $alignment_len);
	$p->line($x,$scale_ypos, $x,$scale_ypos+4);
	$p->text( {align => 'center'}, $x,$scale_ypos+4+$textsize*.2, $i);
}
$p->text( {align => 'center'}, ($rect_x1+$extended_x2)/2,$scale_ypos+8+$textsize+$textsize*.2, "Position in amino acid alignment");


# Call the drawing command and save the image
if ($tree =~ m/(\d+)\:([0-9\.]+)/) {
	print_tree({'name' => $1, 'len' => $2}, 0);
	$p->output($outfile);
}


sub print_tree {
	my $node = shift;
	my $dist = shift;
	my $x1 = $dist * ($width * .25) + $buffer - $linesize * .5;
	$dist += $node->{'len'} * $tree_zoom;
	my $x2 = $dist * ($width * .25) + $buffer;
	
	if ($node->{'name'} =~ m/^\d+$/) {
		my @subnodes = @{$nodes[$node->{'name'}]};
		my @ypos_arr = map(print_tree($_, $dist), @subnodes);
		
		my $y_avg = avg(@ypos_arr);
		my $y_min = min(@ypos_arr);
		my $y_max = max(@ypos_arr);
		
		$p->setcolour(0,0,0);
		$p->line($x2,$y_min, $x2,$y_max);
		$p->line($x1,$y_avg, $x2,$y_avg);
		return $y_avg;
	} else {
		my $y_pos = shift @names_ypos;
		my $y_min = $y_pos - $rect_halfheight + $linesize * .5;
		my $y_max = $y_pos + $rect_halfheight - $linesize * .5;
		$x2 = $x1 + $linesize if ($x2 - $x1 < $linesize);
		
		$p->setcolour(0,0,0);
		$p->line($x1,$y_pos, $x2,$y_pos);
		my $name = $node->{'name'};
		   $name =~ tr/\_/\ /;
		   $name =~ s/^([A-Z])\ /$1\.\ /;
		$p->text($x2+$text_x_adjust,$y_pos+$text_y_adjust, $name);
		
		my $protein_seq = $proteins{$node->{'name'}};
		
		# Grey box representing the gene
		$p->setcolour(200,200,200);
		$protein_seq =~ m/^(\-*)(.*?)(\-*)$/;
		my $protein_start = $rect_x1 + $rect_width * (length($1) / $alignment_len);
		my $protein_end   = $rect_x2 - $rect_width * ((length($3) ) / $alignment_len);
		$p->box( {filled => 1}, $protein_start,$y_min, $protein_end,$y_max);
		
		# White out gapped regions
		$p->setcolour("white");
		while ($protein_seq =~ m/(\-+)/g) {
			my $gap_start = length($`);
			my $gap_end = $gap_start + length($1);
			my $aa_x1 = $rect_x1 + $rect_width * ($gap_start / $alignment_len);
			my $aa_x2 = $rect_x1 + $rect_width * ($gap_end / $alignment_len);
			$p->box( {filled => 1}, $aa_x1,$y_min, $aa_x2,$y_max);
		}
		
		# Mapping of positions between gapped and ungapped
		my @u2g = ();
		my $protein_useq = $protein_seq; $protein_useq =~ tr/\-//d;
		foreach (0..($alignment_len-1)) {
			push @u2g, $_ unless (substr($protein_seq, $_, 1) eq '-');
		}
		
		# Heat map amino acids according to conservation if peptide was found
		foreach my $pep (@peptides) {
			my $pep_start = -1;
			while (($pep_start = index($protein_useq, $pep, $pep_start + 1)) > -1) {
				my $pep_end = $pep_start + length($pep) - 1;
				foreach ($pep_start..$pep_end) {
					my $aa_pos = $u2g[$_];
					my $aa     = substr($protein_seq, $aa_pos, 1);
					next if ($aa eq '-');
					my $aa_x1 = $rect_x1 + $rect_width * ($aa_pos / $alignment_len);
					my $aa_x2 = $rect_x1 + $rect_width * (($aa_pos+1) / $alignment_len);
					my $cons  = $consensus[$aa_pos]->{$aa};
					$p->setcolour(255*$cons, 255-255*$cons, 0);
					$p->box( {filled => 1}, $aa_x1,$y_min, $aa_x2,$y_max);
				}
			}
		}
		
		# Black border around protein in alignment
		$p->setcolour(0,0,0);
		$p->box( {filled => 0}, $protein_start - .5 * $linesize,$y_min, $protein_end + .5 * $linesize,$y_max);
		
		return $y_pos;
	}
}

sub avg {
	my $sum = 0;
	   $sum+= $_ foreach(@_);
	my $avg = $sum / scalar(@_);
	return $avg;
}
sub min {
	my $min = shift;
	foreach (@_) { $min = $_ if ($_ < $min); };
	return $min;
}
sub max {
	my $max = shift;
	foreach (@_) { $max = $_ if ($_ > $max); };
	return $max;
}
sub sum {
	my $sum = 0;
	$sum += $_ foreach (@_);
	return $sum;
}
sub unique {
	my %hash = ();
	$hash{$_} = 1 foreach (@_);
	my @uniq = keys %hash;
	return @uniq;
}