Commit 63b7e9f0 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO

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# 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)
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
(((((((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);
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)
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