Initial commit

d8363b4a · Alexis CRISCUOLO · d8363b4a · d8363b4a · d8363b4a · d8363b4a
Commit d8363b4a authored May 10, 2018 by Alexis CRISCUOLO ⚫
7 changed files
--- a/COPYING
+++ b/COPYING
--- a/README.md
+++ b/README.md
+# C2A / A2C
+
+_C2A_ and _A2C_ are command line programs written in [Java](https://docs.oracle.com/javase/8/docs/technotes/guides/language/index.html) that allow translating and back-translating FASTA-formatted codon and amino-acid sequence files, respectively. These tools were implemented to easily infer multiple sequence alignments at the codon level.
+
+## Compilation and execution
+
+The source codes are inside the _src_ directory and could be compiled and executed in two different ways. 
+
+#### Building an executable jar file
+
+On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (6 or higher) installed, Java executable jar files could be created. In a command-line window, go to the _src_ directory and type:
+```bash
+javac C2A.java A2C.java
+echo Main-Class: C2A > MANIFEST.MF 
+jar -cmvf MANIFEST.MF C2A.jar C2A.class 
+echo Main-Class: A2C > MANIFEST.MF 
+jar -cmvf MANIFEST.MF A2C.jar A2C.class 
+rm MANIFEST.MF C2A.class A2C.class 
+```
+This will create the two executable jar files `C2A.jar` and `A2C.jar` that could be launched with the following command line models:
+```bash
+java -jar C2A.jar [file]
+java -jar A2C.jar [files]
+```
+
+#### Building a native code binary
+
+On computers with the [GNU compiler GCJ](https://gcc.gnu.org/onlinedocs/gcc-4.2.4/gcj/) installed, binaries could also be built. In a command-line window, go to the _src_ directory, and type:
+```bash
+make
+```
+This will create the two executable binary files `c2a` and `a2c` that could be launched with the following command line models:
+```bash
+./c2a [file]
+./a2c [files]
+```
+
+## Usage
+
+Launch _C2A_ without option to read the following documentation:
+
+```
+  USAGE:   C2A  <seq.fna>
+
+  where <seq.fna> is a FASTA-formatted codon sequence file.
+  This  will  output in  stdout the  translation  (standard
+  genetic code) of each sequence in the same format.
+```
+
+Launch _A2C_ without option to read the following documentation:
+
+```
+  USAGE:   A2C  <ali.faa>  <seq.fna>
+
+  where <ali.faa> is a FASTA-formatted multiple amino-acid
+  sequence alignment file  and <seq.ali> a FASTA-formatted
+  file containing  the associated  codon  sequences.  This
+  will  output  in  stdout  the  multiple  back-translated
+  sequence alignment.
+```
+
+## Example
+
+To illustrate the usefulness of _C2A_ and _A2C_, the directory _example_ contains FASTA files from the study of [Drini et al. (2016)](https://doi.org/10.1093/gbe/evw140). The first file _seq.fna_ contains several _Leishmania_ and _Trypanosoma_ codon sequences from the sub-family HSPA1. In order to easily infer an accurate multiple sequence alignment at the codon level, _C2A_ and _A2C_ could be used together with a standard multiple sequence alignment program.
+
+First, using _C2A_ allows creating the file _seq.faa_ that contains the translation of every codon sequence inside _seq.fna_:
+```bash
+C2A  seq.fna  >  seq.faa
+```
+Second, the created `seq.faa`could be used to infer a multiple amino-acid sequence alignment, which is expected to be more accurate than the one inferred from the initial codon sequences. The directory _src_ contains such an alignment inside the file _ali.faa_.
+
+Finally, using _A2C_ allows creating the file _ali.fna_ by back-translating the amino-acid sequences inside _ali.faa_ with the associated codon sequences inside _seq.fna_:
+```bash
+A2C  ali.faa  seq.fna  >  ali.fna
+```
+Following this way, the file _ali.fna_ contains an accurate multiple sequence alignment at the codon level, i.e. the homology is recovered for each codon position.
+
+## Reference
+
+Drini S, Criscuolo A, Lechat P, Imamura H, Skalický T, Rachidi N, Lukeš J, Dujardin JC, Späth GF (2016) Species- and strain-specific adaptation of the HSP70 super family in pathogenic Trypanosomatids. Genome Biology and Evolution, 8(6):1980-1995. [doi:10.1093/gbe/evw140](https://doi.org/10.1093/gbe/evw140).
--- a/example/ali.faa
+++ b/example/ali.faa
+>LinJ.28.2950
+MPWYLFSTTSSPRCALPLPPFYPPNHTQDPKHALALKLSEENTYAHRHTSLSLCALLRNP
+ITTLLPPPPIPHAHTHTTTAAEMTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRV--------------------------------------
+------------------------------------------------------------
+-------------------------------------------
+>LDPBQ7IC8_280037100
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280037000
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280036500
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280036600
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGMMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280036700
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280036800
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LDPBQ7IC8_280036900
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LinJ.28.3000
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LinJ.28.2960
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LinJ.28.3060
+MPWYLFSTTSSPRCALPLPPFYPPNHTQDPKHALALKLSEENTYAHRHTSLSLCALLRNP
+ITTLLPPPPIPHAHTHTTTAAEMTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPMIAVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDRAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDSDKATLNKEI
+DVTLEWLSSNQEATKEEYEHKQKELESVCNPIMTKMYQSMGGA--G--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LmjF.28.2770
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPVISVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENIDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEEDDKAQRDRVEAKNGLENYAYSMKNTLSDSNVSGKLDDSDKATLNKEI
+DAALEWLSSNQEATKEEYEHRQKELESVCNPIMTKMYQSMGGA--AG-----------GM
+PGGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LmjF.28.2780
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNERVDIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPVISVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRALRRLRTACERAKRTL
+SSATQATIEIDALFENIDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEEDDKAQRDRVEAKNGLENYAYSMKNTLSDSNVSGKLDDSDKATLNKEI
+DAALEWLSSNQEATKEEYEHRQKELESVCNPIMTKMYQSMGGA--AG-----------GM
+PGGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LmxM.28.2780
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNDRVEIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPVISVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTISGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKNXKGKNLASSHRSLRRLRTACERAKRTL
+SSATQATIEIDALFDNVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDKAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDTDKSTLNKEI
+DAALEWLSSNQEATKEEYEHKQKELENVCNPIMTKMYQSMGGG--A--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVD-
+>LmxM.28.2770
+------------------------------------------------------------
+----------------------MTFDGAIGIDLGTTYSCVGVWQNDRVEIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFNDSVVQSDMKHWPFKVTTKG
+DDKPVISVQYRGEEKTFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTISGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFTEEFKRKN-KGKNLASSHRSLRRLRTACERAKRTL
+SSATQATIEIDALFDNVDFQATITRARFEELCGDLFRSTIQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQITITNDKGRLSKDE
+IERMVNDAMKYEADDKAQRDRVEAKNGLENYAYSMKNTLGDSNVSGKLDDTDKSTLNKEI
+DAALEWLSSNQEATKEEYEHKQKELENVCNPIMTKMYQSMGGG--A--------------
+-GGMPGGMPD--MSGMSGGAG---PA---GGASSGPKVEEVDX
+>LbrM.28.2990
+------------------------------------------------------------
+----------------------MTFEGAIGIDLGTTYSCVGVWQNERVEIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKYGDPVVQADMKHWPFKVKTKG
+EDKPVISVQYCNEEKIFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFSEEFKRKN-KGKDLSSSHRALRRLRTACERAKRTL
+SSATQATIEIDALFDNVDFQANITRARFEELCGDLFRSTMQPVERVLQDAKMDKRSVHDV
+VLVGGSTRIPKVQSLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNHITITNDKGRLSKDE
+IERMVNDASKYEQADKMQRERVEAKNGLENYAYSMKNTVSDTNVSGKLEESDRSALNSAI
+DAALEWLNSNQEASKEEYEHRQKELESTCNPIMTKMYQSMGGG--A--------------
+-GGMPGGMPD--MSGMGGGAG---PA---AGASSGPKVEEVDX
+>LbrM.28.2980
+------------------------------------------------------------
+----------------------MTFEGAIGIDLGTTYSCVGVWQNERVEIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKYGDPVVQADMKHWPFKVKTKG
+EDKPVISVQYCNEEKIFTPEEISSMVLLKMKETAEAYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKGDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVTFFSEE--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------XXXXFLTYGANQPGWPSR-FRGRARDEKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNHITITNDKGRLSKDE
+IERMVNDASKYEQADKMQRERVEAKNGLENYAYSMKNTVSDTNVSGKLEESDRSALNSAI
+DAALEWLNSNQEASKEEYEHRQKELESTCNPIMTKMYQS---------------------
+-------------------------------------------
+>TvY486_1112330
+------------------------------------------------------------
+----------------------MTYEGAIGIDLGTTYSCVGVWQNERVEIIANDQGNRTT
+PSYVAFTDTERLIGDAAKNQVAMNPLNTVFDAKRLIGRKFSDSVVQADMKHWPFKVTTKG
+DDKPVIQVQFHGETKTFNPEEISSTVLLKMKEVAESYLGKQVTKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKVDDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVAHFTEEFKRKN-KGKDLTTSQRALRRLRTACERAKRTL
+SSAAQATIEIDALFDSVDFQSTITRARFEELCGDLFRGTLQPVERVLQDAKMDKRAVHDV
+VLVGGSTRIPKVMQLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVAPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLNADGILSVSAEEKGTGKRNQIVITNDKGRLSKAE
+IERMVNDAAKYEAQDKAQRERVDAKNALENYAFSMKSTATDPNVGGKLDEADKNTIIEAV
+DGALQWLNNNQEASKEEYEHRQKELEGVCTPIMTKMYQGMGGG--A--------------
+-GGMPGGMPGGMPGGMPGGMGGG-------APSAGPRVEEVDX
+>Tb927.11.11330
+------------------------------------------------------------
+----------------------MTYEGAIGIDLGTTYSCVGVWQNERVEIIANDQGNRTT
+PSYVAFTDSERLIGDAAKNQVAMNPTNTVFDAKRLIGRKFSDSVVQSDMKHWPFKVVTKG
+DDKPVIQVQFRGETKTFNPEEISSMVLLKMKEVAESYLGKQVAKAVVTVPAYFNDSQRQA
+TKDAGTIAGLEVLRIINEPTAAAIAYGLDKADEGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVAHFTEEFKRKN-KGKDLSSNLRALRRLRTACERAKRTL
+SSAAQATIEIDALFENIDFQATITRARFEELCGDLFRGTLQPVERVLQDAKMDKRAVHDV
+VLVGGSTRIPKVMQLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVAPLTLGIETAGGVMTALIKRNTTIPTKKSQIFSTYSDNQPGVHIQVFEGERTMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILSVSAEEKGTGKRNQIVITNDKGRLSKAD
+IERMVSDAAKYEAEDKAQRERIDAKNGLENYAFSMKNTINDPNVAGKLDDADKNAVTTAV
+EEALRWLNDNQEASLDEYNHRQKELEGVCAPILSKMYQGMGGGDAA--------------
+-GGMPGGMPGGMPGGMPGGMGGGMGG---AAASSGPKVEEVDX
+>TcCLB.511211.170
+------------------------------------------------------------
+----------------------MTYEGAIGIDLGTTYSCVGVWQNERVEIIANDQGSRTT
+PSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRKFSDPVVQSDMKHWPFKVITKG
+DDKPVIQVQFRGETKTFNPEEVSSMVLSKMKEIAESYLGKQVKKAVVTVPAYFNDSQRQA
+TKDAGTIAGMEVLRIINEPTAAAIAYGLDKVEDGKERNVLIFDLGGGTFDVTLLTIDGGI
+FEVKATNGDTHLGGEDFDNRLVSHFTDEFKRKN-KGKDLTTSQRALRRLRTACERAKRTL
+SSAAQATIEIDALFDNVDFQATITRARFEELCGDLFRGTLQPVERVLQDAKMDKRAVHDV
+VLVGGSTRIPKVMQLVSDFFGGKELNKSINPDEAVAYGAAVQAFILTGGKSKQTEGLLLL
+DVTPLTLGIETAGGVMTSLIKRNTTIPTKKSQIFSTYADNQPGVHIQVFEGERAMTKDCH
+LLGTFDLSGIPPAPRGVPQIEVTFDLDANGILNVSAEEKGTGKRNQIVITNDKGRLSKAD
+IERMVSEAAKYEAQDKEQRERIDAKNGLENYAFSMKNTVNEPNVAGKIEEADKNTITSAV
+EEALQWLNNNQEASKEEYEHRQKELENLCTPIMTKMYQGMGAG--GGMPGGMPGGMPGGM
+PGGMPGGMPGGMPGGMPGGMPGGMPGGANPSSSSGPKVEEVDX
--- a/example/seq.fna
+++ b/example/seq.fna
--- a/src/A2C.java
+++ b/src/A2C.java
+/*
+  ####################################################################
+  A2C: back-translating a multiple  amino-acid sequence alignment into
+       a multiple codon sequence alignment
+
+  Copyright (C) 2015-2018  Alexis Criscuolo 
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation,  either version 3  of the License,  or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,  but
+  WITHOUT  ANY  WARRANTY;   without  even  the   implied  warranty  of
+  MERCHANTABILITY or  FITNESS FOR  A PARTICULAR  PURPOSE.  See the GNU 
+  General Public License for more details.
+  
+  You should have  received a copy  of the GNU  General Public License
+  along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+  Contact: 
+  Institut Pasteur
+  Bioinformatics and Biostatistics Hub
+  C3BI, USR 3756 IP CNRS
+  Paris, FRANCE
+
+  alexis.criscuolo@pasteur.fr
+  ####################################################################
+*/
+import java.io.*;
+import java.util.*;
+public class A2C {
+    static File aafile, ntfile;
+    static BufferedReader in;
+    static ArrayList<String> fh;
+    static ArrayList<StringBuilder> aa, nt;
+    static int i, c, l, n, x;
+    static String line, aaseq, ntseq;
+    static StringBuilder coseq;
+    public static void main(String[] args) throws IOException {
+	if ( args.length < 2 ) {
+	    System.out.println("");
+	    System.out.println("  USAGE:   A2C  <ali.faa>  <seq.fna>"); System.out.println("");
+	    System.out.println("  where <ali.faa> is a FASTA-formatted multiple amino-acid");
+	    System.out.println("  sequence alignment file  and <seq.ali> a FASTA-formatted");
+	    System.out.println("  file containing  the associated  codon  sequences.  This");
+	    System.out.println("  will  output  in  stdout  the  multiple  back-translated");
+	    System.out.println("  sequence alignment.");
+	    System.out.println(""); System.exit(0);
+	}
+	fh = new ArrayList<String>(); aa = new ArrayList<StringBuilder>(); nt = new ArrayList<StringBuilder>(); i = n = -1;
+	if ( ! (aafile=new File(args[0])).exists() ) { System.err.println("file " + args[0] + " does not exist"); System.exit(1); }
+	in = new BufferedReader(new FileReader(aafile));
+	while ( true ) {
+	    try { line = in.readLine().trim(); } catch ( NullPointerException e ) { ++n; in.close(); break; }
+	    if ( line.startsWith(">") ) { ++n; fh.add(line); aa.add(new StringBuilder("")); nt.add(new StringBuilder("")); continue; }
+	    aa.set(n, aa.get(n).append(line));
+	}
+	if ( ! (ntfile=new File(args[1])).exists() ) { System.err.println("file " + args[1] + " does not exist"); System.exit(1); }
+	in = new BufferedReader(new FileReader(ntfile));
+	while ( true ) {
+	    try { line = in.readLine().trim(); } catch ( NullPointerException e ) { i = -1; in.close(); break; }
+	    if ( line.startsWith(">") ) { i = fh.indexOf(line); continue; }
+	    if ( i >= 0 ) nt.set(i, nt.get(i).append(line));
+	}
+	while ( ++i < n ) {
+	    if ( (ntseq=nt.get(i).toString()).length() == 0 ) continue;
+	    coseq = new StringBuilder(""); l = (aaseq=aa.get(i).toString()).length(); c = -1; x = 0; 
+	    while ( ++c < l ) coseq = ( aaseq.charAt(c) == '-' ) ? coseq.append("---") : coseq.append(ntseq.substring(x, (x += 3)));
+	    System.out.println(fh.get(i)); System.out.println(coseq.toString());
+	}
+    }
+}
--- a/src/C2A.java
+++ b/src/C2A.java
+/*
+  ####################################################################
+  C2A: translating  a  FASTA-formatted  codon  sequence  file  into an 
+       amino-acid one
+
+  Copyright (C) 2015-2018  Alexis Criscuolo 
+
+  This program is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation,  either version 3  of the License,  or
+  (at your option) any later version.
+  
+  This program is distributed in the hope that it will be useful,  but
+  WITHOUT  ANY  WARRANTY;   without  even  the   implied  warranty  of
+  MERCHANTABILITY or  FITNESS FOR  A PARTICULAR  PURPOSE.  See the GNU 
+  General Public License for more details.
+  
+  You should have  received a copy  of the GNU  General Public License
+  along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+  Contact: 
+  Institut Pasteur
+  Bioinformatics and Biostatistics Hub
+  C3BI, USR 3756 IP CNRS
+  Paris, FRANCE
+
+  alexis.criscuolo@pasteur.fr
+  ####################################################################
+*/
+import java.io.*;
+public class C2A {
+    static BufferedReader in;
+    static String line, fh;
+    static int lgt;
+    static StringBuilder sb;
+    public static void main(String[] args) throws IOException {
+	if ( args.length < 1 ) {
+	    System.out.println("");
+	    System.out.println("  USAGE:   C2A  <seq.fna>"); System.out.println("");
+	    System.out.println("  where <seq.fna> is a FASTA-formatted codon sequence file.");
+	    System.out.println("  This  will  output in  stdout the  translation  (standard");
+	    System.out.println("  genetic code) of each sequence in the same format.");
+	    System.out.println(""); System.exit(0);
+	}
+	try { in = new BufferedReader(new FileReader(new File(args[0]))); sb = new StringBuilder(""); }
+	catch ( FileNotFoundException e ) { System.out.println("file " + args[0] + " does not exist"); System.exit(1); }
+	while ( true ) {
+	    try { line = in.readLine().trim(); } catch ( NullPointerException e ) { in.close(); break; }
+	    if ( line.startsWith(">") ) { 
+		if ( ((lgt=sb.length()) > 0) && (lgt % 3 == 0) ) { System.out.println(fh); System.out.println(toaa(sb)); }
+		fh = line; sb = new StringBuilder(""); continue; 
+	    }
+	    sb = sb.append(line.toUpperCase());
+	}
+	if ( ((lgt=sb.length()) > 0) && (lgt % 3 == 0) ) { System.out.println(fh); System.out.println(toaa(sb)); }
+    }
+    static String toaa(StringBuilder cod) {
+	int c = -1, l = cod.length(); StringBuilder aa = new StringBuilder("");
+	while ( ++c < l ) 
+	    switch (cod.charAt(c)) {
+	    case 'A':
+		switch (cod.charAt(++c)) {                                                                                                                                                                                          // A..
+		case 'A': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('K'); continue; case 'C': case 'T': aa = aa.append('N'); continue; default: aa = aa.append('X'); continue; }                                // AA.
+		case 'C': aa = aa.append('T'); ++c; continue;                                                                                                                                                                       // AC.
+		case 'G': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('R'); continue; case 'C': case 'T': aa = aa.append('S'); continue; default: aa = aa.append('X'); continue; }                                // AG.
+		case 'T': switch (cod.charAt(++c)) { case 'A': case 'C': case 'T': aa = aa.append('I'); continue; case 'G': aa = aa.append('M'); continue; default: aa = aa.append('X'); continue; }                              } // AT.
+	    case 'C':
+		switch (cod.charAt(++c)) {                                                                                                                                                                                          // C..
+		case 'A': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('Q'); continue; case 'C': case 'T': aa = aa.append('H'); continue; default: aa = aa.append('X'); continue; }                                // CA.
+		case 'C': aa = aa.append('P'); ++c; continue;                                                                                                                                                                       // CC.
+		case 'G': aa = aa.append('R'); ++c; continue;                                                                                                                                                                       // CG.
+		case 'T': aa = aa.append('L'); ++c; continue;                                                                                                                                                                     } // CT.
+	    case 'G':
+		switch (cod.charAt(++c)) {                                                                                                                                                                                          // G..
+		case 'A': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('E'); continue; case 'C': case 'T': aa = aa.append('D'); continue; default: aa = aa.append('X'); continue; }                                // GA.
+		case 'C': aa = aa.append('A'); ++c; continue;                                                                                                                                                                       // GC.
+		case 'G': aa = aa.append('G'); ++c; continue;                                                                                                                                                                       // GG.
+		case 'T': aa = aa.append('V'); ++c; continue;                                                                                                                                                                     } // GT.
+	    case 'T':
+		switch (cod.charAt(++c)) {                                                                                                                                                                                          // T..
+		case 'A': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('X'); continue; case 'C': case 'T': aa = aa.append('Y'); continue; default: aa = aa.append('X'); continue; }                                // TA.
+		case 'C': aa = aa.append('S'); ++c; continue;                                                                                                                                                                       // TC.
+		case 'G': switch (cod.charAt(++c)) { case 'A': aa = aa.append('X'); continue; case 'C': case 'T': aa = aa.append('C'); continue; case 'G': aa = aa.append('W'); continue; default: aa = aa.append('X'); continue; } // TG.
+		case 'T': switch (cod.charAt(++c)) { case 'A': case 'G': aa = aa.append('L'); continue; case 'C': case 'T': aa = aa.append('F'); continue; default: aa = aa.append('X'); continue; }                              } // TT.
+	    default: aa = aa.append('X'); ++c; ++c; continue;
+	    }
+	return aa.toString();
+    }
+}
--- a/src/Makefile
+++ b/src/Makefile
+GCJ=gcj
+GCJFLAGS=-fsource=1.6 -march=native -msse2 -O3 -minline-all-stringops -fomit-frame-pointer -momit-leaf-frame-pointer -fstrict-aliasing -fno-store-check -fno-bounds-check -funroll-all-loops -Wall 
+OTHERFLAGS=-funsafe-math-optimizations -ffast-math
+
+all: C2A A2C
+
+C2A: C2A.java
+	$(GCJ) $(GCJFLAGS) --main=C2A C2A.java -o c2a
+
+A2C: A2C.java
+	$(GCJ) $(GCJFLAGS) --main=A2C A2C.java -o a2c