diff --git a/align.sh b/align.sh
new file mode 100644
index 0000000..8a21782
--- /dev/null
+++ b/align.sh
@@ -0,0 +1,10 @@
+#usage: bash align.sh
+#aligns sequences for bioinformatics purposes
+
+for x in *.fasta
+do sed -e '$s/$/\n/' -s sporecoat*.fasta > combinedspores.fasta; sed -e '$s/$/\n/' -s transporter*.fasta > combinedtransporter.fasta
+done
+
+/afs/nd.edu/user9/svandext/local/bin/muscle3.8.31_i86linux64 -in combinedspores.fasta -out sporesaligned.afa
+/afs/nd.edu/user9/svandext/local/bin/muscle3.8.31_i86linux64 -in combinedtransporter.fasta -out transporteraligned.afa
+
diff --git a/gene_sequences/combined.fasta b/gene_sequences/combined.fasta
new file mode 100644
index 0000000..3d09656
--- /dev/null
+++ b/gene_sequences/combined.fasta
@@ -0,0 +1,52 @@
+>Q8XVY0_RALSO/26164
+TTTTFSVSTTVNATCVINSASALTFAAFDPSQGAQASTSSISVNCTNTTPFNIGLNAGTGTGATVASRVMTSGANTLTYSLYQDSGHASVWGNTVGTNTVAGTGAGMAAGNAITKTVYGLIPSQPNTVPGNYADTVTVT
+>Q0BSH7_GRABC/37169
+TTTTFQVTATVQASCIIQATNLSFGNYSGSQTDATSTIQVTCTNSTPYNVGLSAGTGSGATVSNRKMSLNSTSALPYALYSDASRSTNWGNTPNQDTVSGTGNGSAQSLTVYGRIQTGNYPTPGSYADTITAT
+>Q0AAK3_ALKEH/24160
+DTATFDVTATVDPTCTVDADNLVFGTYDPFSDTPLDENSEIRVQCTSDTPYDIGLDDGDNTGAEGERRMALADESDFLEYDLYHDNHGGTSWGDIDSGAELTGLSGTGSEQSYVVYGRIFAEQSVAVGNYVDTIEVT
+>Q8XPY6_RALSO/36170
+KTTTFTVSLTLQADCSISANALNFGTQGVLAANVDQTATLSVTCSNTAPYNVGFDAGTTTGSTIAARLLAGSGAATVGFQLYSDSARTQIWGNTVGTDTVSGTGSGTAQVLTVYGRVPSQNSPAAGTYSTTITAT
+>Q63W79_BURPS/31169
+ATATFTVSLTIQANCTISANALSFGTNGVLATAVNQQTTLSVTCSNTTSYNVGLDAGNVSGSTVSSRLLAGTTTGNTSTTVSFQLYQDSGHTTIWGNTVGTNTVSGTGNGTAQTLSVYGQVPAQTTPKPDTYESTVTAT
+>Q7CVQ4_AGRFC/27162
+ATTNFNVQITIQAACQINSAGNLDFGTNGVIGAPIDVTSQIVVQCTASTPFSLGLSAGAGSGATVANRLMTSAAGATISYSLYTTAAHSTVWGNTVGTDRQTGTGTGAPQNFTVFGRVPAQTTPAVGVYTDTVTAT
+>Q985D5_RHILO/27162
+ATGNMTVRITIQAECKVQTATDMDFGTNGVIDANVDQTSTISVQCTNSTPYNVGLSAGVGAGATVAVRKMTGPAAAVLNYSLYRDVARAQLWGTTIGTDTVAGTGNGAAQPLTVYGRVPPQTTPGAGVYTDTVAIT
+>A6X8A6_OCHA4/27162
+ATGNMNVRITIQAECKIVTATDLDFGTKGVIDVNVDQTSTISVQCTNGTPYTVGLSAGGGAGATVAMRKMTGAASATINYTIYRDAARTQVWGVTAGTDVVSGTGNGNAQSITAYGRVPAQTTPAPGVYSDVVSVT
+>A9CH19_AGRFC/182313
+TQVPFTVSAAVAPTCIISAQNINFGSHGVLNTAVDANGAINLTCTNGLNYSVALNGGLSNSPPAARQMVQGAASIIYGLYRDVSRTNVWGSAAGQIATGTGNGSLQTLTVFGRVPAQNTPAPGNYADTVVVT
+>Q985D8_RHILO/205338
+DRPTFTINAIVPANCLLAIQNIDFGSNGILGANVDATGGVSITCTPGTPYTVSLSNGTTGSAPTARKMSKGVETVTYGLYKDNARSQVWGDAAMPGSTVAGSGSGAAQNLTIYGRVPAQTTPSAGVYTDTVVVT
+>A7H7Q6_ANADF/25150
+ATAQFQVTATVVKKCKISATTIAFGNYDPATILSAEGTLTLKCTKGTLYSVALDGGSTGSRQMTQAAEVLDYELYSDAGHTAVWPSTAAAPSVAAAGADEALIIFAQVPADQYPAPGAYADTVTAT
+>Q2IFL0_ANADE/27162
+ATATLDVTATVVPSCTIAATPVAFGSYDPLVTNAATALDAQGTVTVTCTTGTAYTVGLGAGNSGSGSRAMQHASIAGAQLPYELYQEAARTTVWDSTVMQAGTAASITPVQYTVYGRIPAAQNVPTGNYADAVVAT
+>Q0C623_HYPNA/23151
+ANGTLDVQATVVNTCVVLTAPVVFASVGLDEVTANGSITVNCTNTSAFTVALDGGDSGDISARSLTHASLPASFNYQLYTDAGLTTVWGDGVTGSQANGSGPSQTLTVYGRTTSTPDTAGAYADEVQVT
+>Q63W78_BURPS/193326
+TFAFTASATVVNDCFINATNVAFGSTGVIQGALTATGTISAQCTNGDAFRIALNGGASGNVAARAMQRTGGGGAVNYQLYLDAAHSTIWGDGTAGTSTATGTGSGLSQSLTVYGQVPAQTTPAPGTYSDTITAT
+>Q8XVY3_RALSO/23163
+VLVALASWAPGALAVSCSVSANALSFGAYNTTSNLTGTTTVTITCGAWGGASSINYTLSASVGSGTYANRQVLNGSNVIAYNLYTTSADTSIWGDGNGDGTVTLSGTVTKQVGTVNLTIYGKINGGQNVVPGSYATTIPIT
+>Q8XPY9_RALSO/25163
+ASAQSCSVASASLNFGSISPVQAGNTDTSTTLTVSCSGFLLQGTVARACLNLGVGSGDTGISPRVLSAGANQLQYNLYADSARSVVWGGRTTPATPAIQVDVSLGLLGFGSATVTVYGRVPGGQTTVPAGAYTQSFSGT
+>A9CH19_AGRFC/11158
+IAAAFVASPVLAQSCTFSMSDMNFGFVNLAGGAAVDTTATLSVTCNNPLSLALSIRICPNINAGGGGQSGGIRRMLQGSNILNYQLYQTSARTTAWGSVTQPALGAPPPIDMALPLLINSTTRTVYGRINAGQASAARGLYLSSFAGG
+>Q985D8_RHILO/37183
+SAALLLPTVAWAQSCSFGVSAMNFGLVDTLSGSSSNSTATLSVNCTGLLLQRILVCPNLGTGSGGATASARQMLSGANDLNYQLYSDSARSVVWGSYAWPYPPTAPGFALTLNVLGSGSASQTIYGAILGGQATAVPSTYLSTFSGS
+>Q3A2W0_PELCD/10150
+IIVLLFAVDAYAFHCEVTTTPVSFGAYDVFSSFSLDTTGRISVSCNNPEKKRMPVTISISRGAANSFSPRQMRRIGGSDRMDYYLFVDASRTAVWGDGTGGSSTYVGMIDRTSPLNVPIYGRIPARQNLRAGSYQDILVVT
+>A7H7Q5_ANADF/16150
+APRAVDAAQPPSPGPSCSVSAGSVAFGAYDPLSPTHLDSTGTIGLTCAVRQLVTISLGTGQSGTFARELRGPGGAALRYDLYTDATRTQVWGDGTAGTATWPFETERGRYVPVYARVLAGQDVPAGPYSDTIVVT
+>Q2IFK8_ANADE/19157
+ATALSLVAPAAARAASCSLTMGTSIAFGAYDPLSPVPLTTTGMLQYRCSRGQPIRITFTAGSSGDVYARTLRQGPWTLAYNLYADAGFGTVWGDGTGGTAAAPAVTTLSNGLTVAYVFGRIPARQEPPVGPYSDTIVVT
+>Q1D5L1_MYXXD/13153
+AVAGVCGLLPGLAGAVCQIRSTIGVSFGTYLTTDLLPRDSAGSITYRCEGQITPITIDFSAGGSGTPLARSMAGPGAQRLEYNLYVDATRLIVWGNGTSGTGRYGPVVPLFGVEVTVPIFGRIPAGQAIPAGAYADTVVMT
+>Q60C08_METCA/20167
+LLACPKISDADPYQCDIGNISVPHAVYDPTDSNPNSSGVGTVGITCHLKNAKQTQQVQYTIALSRGSSGSYNPRRMSGGRGSLGYNLYLDAARVTIWGDGSGGTFPLRGTLLLNPTTPVQQVIHNIYGLIPPLQDVYAGTYTDTVTIT
+>Q0AAK6_ALKEH/8153
+SLFLVAAGSGSAQAYTCSISADPLAFGQYDPITGAQVDGASEVSVSCSLLGLVSLLVSYEISLDPGTGGSYHPRALSSATDTLDYNLYVDTARTEIWGDGTDDTATVTDSYTLGVLTVTRYYPVYGRVFADQNVAAGVYDDTITAT
+>Q12FX3_POLSJ/50194
+TWGVLLAAGTAHATISCSVSGNGFTSVYDPISTVPNDNVSSVTINCSRASGDPTTTTYSLASTNGLYPQGQNNRAYYPTNKYLKYDIYKDAAYSSRWGPGGSAPFTGTLNFGSGTSASLTLPYYNRVAAQQSAVAADYTDTMTAT
+>A1VIJ0_POLNA/19170
+ALFLLLATAGPAQAGSCTVGSSGLAFGAYQPLTFAGKLTSSAVTSNASISVVCTGIASGGAYSIALGPSTTGSGDRISTRYLGNSNGGDDMSFNIYTSASYSTVWGNGTTGGLVGGSIPVGDSNQSQPVYGRIAASQNTLRAGSYSGSLTMT
diff --git a/gene_sequences/combined2.fasta b/gene_sequences/combined2.fasta
new file mode 100644
index 0000000..c75277a
--- /dev/null
+++ b/gene_sequences/combined2.fasta
@@ -0,0 +1,8 @@
+>LACY_CITFR/1412
+MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQPIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNAGAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVILALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIMSVRIIGSHSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRRE
+>LACY_KLEOX/6416
+LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQPVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSSRSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALILGVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFDQQFANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIMSVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQLSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTLKGSKTLLPATA
+>RAFB_ECOLX/4415
+ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQPLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSAGAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLLLLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFDQQFAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIMTIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQLAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLSSSPGIVHPSVE
+>A0A026RKY7_ECOLX/4411
+NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRFKDKDHQCIAADAGGVKKEDFIAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPV