Initial commit

README.md

+# REQ
+
+_REQ_ is a command line program written in [Java](https://docs.oracle.com/javase/8/docs/technotes/guides/language/index.html) that allows estimating the rate of elementary quartets (REQ) for each internal branch of a phylogenetic tree from a distance matrix, as described by [Guénoche and Garreta (2001)](https://doi.org/10.1007/3-540-45727-5_5).
+
+## Compilation and execution
+
+The source code of _REQ_ is 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, a Java executable jar file could be created. In a command-line window, go to the _src_ directory and type:
+```bash
+javac REQ.java 
+echo Main-Class: REQ > MANIFEST.MF 
+jar -cmvf MANIFEST.MF REQ.jar REQ.class 
+rm MANIFEST.MF REQ.class 
+```
+This will create the executable jar file `REQ.jar` that could be launched with the following command line model:
+```bash
+java -jar REQ.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, a binary could also be built. In a command-line window, go to the _src_ directory, and type:
+```bash
+make
+```
+This will create the executable binary file `req` that could be launched with the following command line model:
+```bash
+./req [files]
+```
+
+## Usage
+
+Launch _REQ_ without option to read the following documentation:
+
+```
+  USAGE:  REQ <dfile> <tfile> [-v]
+
+  <dfile>  a distance matrice file  in either PHYLIP lower-
+           triangular or square format
+  <tfile>  an unrooted  binary phylogenetic  tree file with
+           no confidence value at branches in NEWICK format
+  -v       verbose mode
+
+```
+
+## Example
+
+The directory _example_ contains two files from the study of [Garcia-Hermoso et al. (2018)](https://doi.org/10.1128/mBio.00573-18):     
+* _matrix.d_: a distance matrix in PHYLIP square format estimated from 22 _Mucor circinelloides_ f. _circinelloides_ genomes,
+* _tree.t_: the associated Minimum Evolution phylogenetic tree in NEWICK format.
+
+The following command line writes into the file _tree.req.t_ the phylogenetic tree from _example/tree.t_ with the rate of elementary quartets at each internal branch estimated from the distance matrix _example/matrix.d_:
+```bash
+REQ  example/matrix.d  example/tree.t  >  tree.req.t
+```
+
+## References
+
+Garcia-Hermoso D, Criscuolo A, Lee SC, Legrand M, Chaouat M, Denis B, Lafaurie M, Rouveau M, Soler C, Schaal JV, Mimoun M, Mebazaa A, Heitman J, Dromer F, Brisse S, Bretagne S, Alanio A (2018) Outbreak of invasive wound mucormycosis in a burn unit due to multiple strains of _Mucor circinelloides_ f. _circinelloides_ resolved by whole-genome sequencing. MBio, 24;9(2):e00573-18. [doi:10.1128/mBio.00573-18](https://doi.org/10.1128/mBio.00573-18).
+
+Guénoche A, Garreta H (2001) Can we have confidence in a tree representation? _In_: Gascuel O, Sagot MF (eds) Computational Biology. Lecture Notes in Computer Science, vol 2066. Springer, Berlin, Heidelberg. [doi:10.1007/3-540-45727-5_5](https://doi.org/10.1007/3-540-45727-5_5). [[pdf]](http://iml.univ-mrs.fr/editions/biblio/guenoche/QualiTree-1.pdf)

example/matrix.d

+ 22
+P07_621_SLS     0.00000000 0.02865660 0.02870160 0.02878250 0.03950280 0.03988420 0.04011750 0.04016660 0.03901690 0.03900900 0.03904710 0.03898010 0.03899590 0.03895910 0.03899060 0.03892640 0.03951620 0.03908920 0.03908920 0.03895390 0.03892510 0.03892380
+1006PHL         0.02865660 0.00000000 0.00521582 0.00512027 0.03869940 0.03915910 0.03936560 0.03941090 0.03840960 0.03840700 0.03841730 0.03833760 0.03835940 0.03831570 0.03836200 0.03831830 0.03885310 0.03844440 0.03843530 0.03829910 0.03828620 0.03829780
+P08_701_BU2_PER 0.02870160 0.00521582 0.00000000 0.00277604 0.03888190 0.03931120 0.03951210 0.03953220 0.03862280 0.03862150 0.03860070 0.03850890 0.03854890 0.03850630 0.03853730 0.03848310 0.03903660 0.03860720 0.03859040 0.03849340 0.03848310 0.03847920
+P01_617_BU1_SLS 0.02878250 0.00512027 0.00277604 0.00000000 0.03885570 0.03929930 0.03948950 0.03952680 0.03858650 0.03858260 0.03858390 0.03850760 0.03855540 0.03853210 0.03853470 0.03848690 0.03904320 0.03860590 0.03859940 0.03850110 0.03848690 0.03848050
+P11_702_BU2_PER 0.03950280 0.03869940 0.03888190 0.03885570 0.00000000 0.00167453 0.00178869 0.00187529 0.01829370 0.01827060 0.01831740 0.01824630 0.01831260 0.01823540 0.01825780 0.01824690 0.01881830 0.01830400 0.01829310 0.01823110 0.01822690 0.01825300
+E01_615_SLS     0.03988420 0.03915910 0.03931120 0.03929930 0.00167453 0.00000000 0.00190845 0.00200267 0.01876060 0.01873950 0.01878480 0.01871840 0.01878110 0.01872150 0.01871530 0.01872280 0.01866770 0.01877920 0.01877670 0.01872400 0.01871530 0.01873820
+P04_601_BU1_SLS 0.04011750 0.03936560 0.03951210 0.03948950 0.00178869 0.00190845 0.00000000 0.00028225 0.01891870 0.01889250 0.01891060 0.01884950 0.01894490 0.01887500 0.01885380 0.01886690 0.01899250 0.01892810 0.01892370 0.01887000 0.01886690 0.01888190
+P04_559_BU1_SLS 0.04016660 0.03941090 0.03953220 0.03952680 0.00187529 0.00200267 0.00028225 0.00000000 0.01895120 0.01892560 0.01895620 0.01888870 0.01898690 0.01891810 0.01889750 0.01890930 0.01903140 0.01897680 0.01896500 0.01891560 0.01890740 0.01892930
+P05_600_BU1_SLS 0.03901690 0.03840960 0.03862280 0.03858650 0.01829370 0.01876060 0.01891870 0.01895120 0.00000000 0.00038241 0.00165844 0.00158976 0.00160947 0.00153078 0.00140824 0.00158766 0.00198330 0.00144933 0.00150698 0.00154334 0.00155120 0.00156509
+P05_598_BU1_SLS 0.03900900 0.03840700 0.03862150 0.03858260 0.01827060 0.01873950 0.01889250 0.01892560 0.00038241 0.00000000 0.00169672 0.00163578 0.00164078 0.00157007 0.00145350 0.00162498 0.00203393 0.00149000 0.00154203 0.00159317 0.00160027 0.00161183
+P04_603_BU1_SLS 0.03904710 0.03841730 0.03860070 0.03858390 0.01831740 0.01878480 0.01891060 0.01895620 0.00165844 0.00169672 0.00000000 0.00043542 0.00161920 0.00154701 0.00145558 0.00147774 0.00215112 0.00160815 0.00165264 0.00152371 0.00154675 0.00154937
+P04_602_BU1_SLS 0.03898010 0.03833760 0.03850890 0.03850760 0.01824630 0.01871840 0.01884950 0.01888870 0.00158976 0.00163578 0.00043542 0.00000000 0.00153496 0.00147748 0.00137866 0.00139526 0.00206551 0.00152607 0.00158293 0.00144881 0.00147226 0.00147539
+P06_032_BU1_SLS 0.03899590 0.03835940 0.03854890 0.03855540 0.01831260 0.01878110 0.01894490 0.01898690 0.00160947 0.00164078 0.00161920 0.00153496 0.00000000 0.00028128 0.00133800 0.00144543 0.00195214 0.00148531 0.00156535 0.00136725 0.00144673 0.00145871
+P06_023_BU1_SLS 0.03895910 0.03831570 0.03850630 0.03853210 0.01823540 0.01872150 0.01887500 0.01891810 0.00153078 0.00157007 0.00154701 0.00147748 0.00028128 0.00000000 0.00125210 0.00137970 0.00190122 0.00144283 0.00150959 0.00129487 0.00137736 0.00138618
+P02_783_BU1_SLS 0.03899060 0.03836200 0.03853730 0.03853470 0.01825780 0.01871530 0.01885380 0.01889750 0.00140824 0.00145350 0.00145558 0.00137866 0.00133800 0.00125210 0.00000000 0.00126652 0.00191809 0.00145298 0.00150698 0.00136156 0.00143294 0.00144100
+P12_579_STR     0.03892640 0.03831830 0.03848310 0.03848690 0.01824690 0.01872280 0.01886690 0.01890930 0.00158766 0.00162498 0.00147774 0.00139526 0.00144543 0.00137970 0.00126652 0.00000000 0.00209039 0.00155434 0.00161315 0.00144283 0.00151273 0.00152162
+P05_622_BU1_SLS 0.03951620 0.03885310 0.03903660 0.03904320 0.01881830 0.01866770 0.01899250 0.01903140 0.00198330 0.00203393 0.00215112 0.00206551 0.00195214 0.00190122 0.00191809 0.00209039 0.00000000 0.00175683 0.00181076 0.00172423 0.00178284 0.00178949
+P10_703_BU2_PER 0.03908920 0.03844440 0.03860720 0.03860590 0.01830400 0.01877920 0.01892810 0.01897680 0.00144933 0.00149000 0.00160815 0.00152607 0.00148531 0.00144283 0.00145298 0.00155434 0.00175683 0.00000000 0.00036705 0.00122665 0.00130622 0.00131190
+P09_704_BU2_PER 0.03908920 0.03843530 0.03859040 0.03859940 0.01829310 0.01877670 0.01892370 0.01896500 0.00150698 0.00154203 0.00165264 0.00158293 0.00156535 0.00150959 0.00150698 0.00161315 0.00181076 0.00036705 0.00000000 0.00129074 0.00135845 0.00137088
+P03_594_BU1_SLS 0.03895390 0.03829910 0.03849340 0.03850110 0.01823110 0.01872400 0.01887000 0.01891560 0.00154334 0.00159317 0.00152371 0.00144881 0.00136725 0.00129487 0.00136156 0.00144283 0.00172423 0.00122665 0.00129074 0.00000000 0.00030335 0.00031354
+P05_599_BU1_SLS 0.03892510 0.03828620 0.03848310 0.03848690 0.01822690 0.01871530 0.01886690 0.01890740 0.00155120 0.00160027 0.00154675 0.00147226 0.00144673 0.00137736 0.00143294 0.00151273 0.00178284 0.00130622 0.00135845 0.00030335 0.00000000 0.00032861
+P03_592_BU1_SLS 0.03892380 0.03829780 0.03847920 0.03848050 0.01825300 0.01873820 0.01888190 0.01892930 0.00156509 0.00161183 0.00154937 0.00147539 0.00145871 0.00138618 0.00144100 0.00152162 0.00178949 0.00131190 0.00137088 0.00031354 0.00032861 0.00000000

example/tree.t

+(((((((P10_703_BU2_PER:0.000157849066,P09_704_BU2_PER:0.000209200934):0.000483122851,P05_622_BU1_SLS:0.001116966803):0.000018368078,((P05_599_BU1_SLS:0.000159586258,P03_592_BU1_SLS:0.000169023742):0.000015792325,P03_594_BU1_SLS:0.000128336869):0.000462006451):0.000081437521,(((P11_702_BU2_PER:0.000615002481,((P04_601_BU1_SLS:0.000117392803,P04_559_BU1_SLS:0.000164857197):0.000925936953,E01_615_SLS:0.000884566733):0.000161626490):0.008730158578,(((P08_701_BU2_PER:0.001390856250,P01_617_BU1_SLS:0.001385183750):0.001280565582,1006PHL:0.002499367591):0.011475862713,P07_621_SLS:0.014634622105):0.015451073655):0.008164485602,(P05_600_BU1_SLS:0.000172301484,P05_598_BU1_SLS:0.000210108516):0.000603348539):0.000010417106):0.000045431349,(P04_603_BU1_SLS:0.000255598014,P04_602_BU1_SLS:0.000179821986):0.000552675249):0.000029208891,(P06_032_BU1_SLS:0.000173131711,P06_023_BU1_SLS:0.000108148289):0.000554756800):0.000022656931,P02_783_BU1_SLS:0.000592772460,P12_579_STR:0.000673747540);
+

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
+MAIN=REQ
+EXEC=req
+
+REQ: REQ.java
+	$(GCJ) $(GCJFLAGS) --main=$(MAIN) $(MAIN).java -o $(EXEC)