Commit b0131d06 authored by Raquel Bromberg's avatar Raquel Bromberg
Browse files

readme.txt updated. Examples directory modified. Output statements from...

readme.txt updated. Examples directory modified. Output statements from programs reduced. All programs and files not involved in the core SlopeTree routines removed. Some minor code cleanup.
parent a107015b
......@@ -9,4 +9,18 @@ mtax
rapidnj
sttag
tmerg
archaea_run_no_filtering.sh
gc.prt
script_cm.sh
script_stmif.sh
buildconcat.cpp
genome_mapped.txt
readme_conflict.txt
script_do_sttagg.sh
script_strun.sh
buildconcat_output_aligned.txt
merge_hgt_pairs_files.cpp
script_do_tmerg.sh
buildconcat_output.txt
rzs.cpp
script_filter.sh
This diff is collapsed.
>gi|189485766|ref|YP_001956706.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MWNEIIIELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYEPLIQNILKAKTGKAVGLQFQI
VASKLLAEPVIKDEKPKAQLIKKTKFTGNPYFKNPAEFTKFAKETTKKEIEISIGQKVMTSMPTKYGAKD
VITFSILNNKMFAYPNDKRKNAKVKMDIRFSNDTVKTFDLYRGQLETRGKGYGQLTTTHAKILLAVIHIW
QEQGCKFADEGQACYVNTTVREIAKKLGYKSFSGADHERLLQKTKDLADLPMVIADRKEAHSFTILYDVS
THVIEDSEGNDTNRRTISIVFNPFIAKQLYDRKVILRKPQCYKIKNPTAIKFLLCYDKRIIKGFNLKMNI
SEVANDLEIETNKTSNIITNIKNAFQELNGYELNDSYSLHVELVKEGKEWIVIAERISKEKQQPLKALLA
>gi|189485767|ref|YP_001956707.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKKLICFVMLGCFVLTFVSCGKRSAMLQDVASVKIEEVKLENGENKTPPPDDPAPEDPETITKADRRVGI
IAGMACMAIAFTGLAIYWMCCGSRKPFEFQVPQDEQNEKPDSEIPKLDNEVPEKPLVDANQDKSELNA
>gi|189485768|ref|YP_001956708.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKFKKVICVYLTLVLFLTGCENLKSQIRGNQNTDASADQQTGNIIKSDNNGIIEKEETKKLDDKVIGLVV
GDEKEKTSSKEPELRWQDKAKKYAGDAVHFLYEHKEQVYFVGIAVIYLLWKERLFQQQNHQDQMQWHLAQ
IQQLQQAQDQIQQMPVQDQIQYLQQLQNHFLQAQFNLQQLNQDPNLIQQFQQVQDQIQNGIGQLQAQVQQ
QIQPQLAQLQLG
>gi|189485769|ref|YP_001956709.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
>gi|189485770|ref|YP_001956710.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKFKKALCVYLTIVLFLTGCENLKSRIRGNQNTDASADQQTGNIIKSGNNGIIEKEETKELDGKSFGLDA
NGNGSSLQGENTEKETPSEEPELMWQDKAKKYAGDAGHFLYEHKGKIAFAVVVVAGVYWFGIRPINGLPA
QPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPPSQPPAQPLLPV
QPLLHVRPEVLQLRQEQALQQYQQQQHEIEELFVPDAVDLFAALGADMTVLDVMLSELRSQITQLYRLQV
RQLQEQLRLQEPQAQEQLLQRQLQERLILAQERQDLLQLRINNLRRHFRQYQAMPFLQIEYLEYQHRLTQ
QLLQQAQQQVQQRQEQQLAELAEQAQQVQQRQEQQLAELAEQAQQLAEQEQQQEQQLAELAEKL
>gi|189485771|ref|YP_001956711.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MRDILMIKIKDKYKLVENIFPINNPFRSSRTVQKALKIINKNFVCNIIVLSLLLCSCGKKQALLNTAITE
KSEVVSELKSELAKIQKELKEKKEKLIEVQEELEKAIEVQEELEKENWQNLWELYDNRMGFFLLGLLTAD
LIVLGCICCTMCSCC
>gi|189485772|ref|YP_001956712.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MEYKKETDYYENDMRHTADAPKLEKRLRKSLNVFGLILLVLAVYLFGSFLLCSCYRRGVVGGVVADNNAV
LPDAVTELKSDKKLINGAGLSLSERSVVAEPFRFGVIVPVVNNDG
>gi|189485773|ref|YP_001956713.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKKIIILLVVFLMFFGCYKKPITNIPVPEEIEEIKIPDVYYFSDMFTACNCFLAISTLFFLATVMFAGYS
FLGKDFDINDYRRPVELGNRIVPQRGNNI
>gi|189485774|ref|YP_001956714.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKKIFAVILMLSVFLSGCHRKVITGISKNENDVPTSTNTPAPEPTSTPMPTSTPAFMDCFPKYKAPSSTP
APLDADDYYDNWTKCVLLYVDDDGNWVNGKHKHSEAHKRLLLKDL
>gi|189485776|ref|YP_001956715.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MWNEIITELKEKIPTEWLEPIKEESFKDDILTLAVPDTYYAQKYETDYKPLIQNILKAKTGKAVGLQFQI
VASKLLAEPVIKDEKPKTQLMKKTKFNGKPYFENPAEFVSIAKAASQVKETDIKNAELTSMPNKYGITNV
ASFSLLDSKFFTYPNDKRKKTKVEMPVRFSNGVVKVYNLYRGQFAINDNGYGQLTTTHAKIFFAIIHIWQ
KQNSRYADNKGFYAVVDISMRELAKQLGYQKVSGADYRRLLQRVKELVDFPMILSDGRVAHTFTFLNSAI
GRTVHQSGKNKLMLRLTLNPFISKQFYERNVILRNPQCYKIKNPTAFKFLLCYDKRVVKGNNLKLNIYEV
ANDLELNISKLCHGVSVLKVAFRELNGYELNDSYRLYVELVKEEREWIVIAERISKEKQQPLKALLA
>gi|189485777|ref|YP_001956716.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MKLKKALCVYLTIVLFLTGCENLKSQIRGNQNTVASADQPTGDIIKSDNSGIIEKQKEKESDLKKIENNV
DNPNGDNGGDNNGDNPNGDNGGDNPNGDNGGDNNGDSSQHKSSSEANGKDLRGWLWDHKGSISGIVLASA
VVIGAIGFWGGQPNVCAVNYFYVPQAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQV
QVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQENQAQVQVPAVQGNQN
PNLVYFDIHSGRYIPGNQNPNLVYFDIHSGRYIPIVRGNPNPILVVQGNLYQVQGNESPFPVLLVEENQV
QVPAVQELPSQQQLQRIQNRLDQLQGQLRNLESHAIFQFQQIQVEAEALQLHNEQYIQLIGSIVDDPLYP
QLNLQFQQICQILRHSHSLQLYDIGFHIFLMREILDHHLHLTARNLPDVYGPPPRWEALRVQEQLERHNQ
QLNQLYQQIEGRLVIEQSVLGARPDSQQRQQELREFNELAIQLQEHQRRIEALLKWLI
>gi|189485778|ref|YP_001956717.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MTAVKFKKIFAVILMLSVFLSGCQRQVITGVSKNENDVSTSTNTPVPEPTPTPTPAPEPTPTPTPVPEPT
PTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPTPTPVPEPTPAFMDCFPKYEAPLSTPAPLDEDDYYDNRV
KWALSHVDDDGNWVNGKHSEAPKCLLVDYYNKF
>gi|189485780|ref|YP_001956718.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MWNEIKTELTEKIPTIWLEPVKEESFKDDILMLNVPNRYYAEKYKTDFKELIQSVIKTKIGKDIGLQCQI
ELLPEPITKDKKPKTTSKTPLIKETKFNGKPYFESPAELTEISKEISQAKEIDVDNTKLTSMPVKYSIKD
VVSFSLLNSKMFTYPNDKRKKTKVEINIRFNNGTIKPLDLYRGQLDFNDEGYGQLTTTHAKIFLAITHIW
QKQGCKFANNSYLAVVDISIRELAKQLGYQKFSGADYKRLLRKTKELADFPMILADMYEAHTFTLLYDVS
NHKLKKSRNNKNMLRILINPFIAKQLYERKVILRNPQCYKIKNPTAIKFLICYDKRIIKGNNLRLNIFEI
ANDLEVNINNITSVAENLKNAFQELNGYELNDSYSLHVELIKENKEWIVVADRVLKEKQQSLKVNCRTDI
ECEA
>gi|189485781|ref|YP_001956719.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MLSLKDNKKSFFSLMCLFFLVVCGCHSAKEFRDGYITGLADGYALSVNEFKYNAELAKIKDEFDWSKVDF
KSEMKMYLDENKDIEKKVYDDYVKNGRKV
>gi|189485782|ref|YP_001956720.1| hypothetical protein [uncultured Termite group 1 bacterium phylotype Rs-D17]
MPTPTPPLTPASPEPASQDKLKKIALFCPPLTQLMFIYGLGLVEGAIQASLPYLFSSPTIISTLSIMFAN
MPIVGAMWFALFAYRSEVSTLSNVLDWSLPALLVFGEFLYFCGVGAVSPFSHWLWSIDPV
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