**C.** If at least one of the four required binaries (step A) is not available on your `$PATH` variable, edit the file `JolyTree.sh` and indicate the local path to the mash, gawk, FastME and/or REQ binary(ies) (approximately between lines 100 and 200):
**C.** If at least one of the four required binaries (step A) is not available on your `$PATH` variable, edit the file `JolyTree.sh` and indicate the local path to the `mash`, `gawk`, `FastME` and/or `REQ` binary(ies) (approximately between lines 100 and 200):
@@ -130,52 +130,49 @@ Launch _JolyTree_ without option to read the following documentation:
## Example
In order to illustrate the usefulness of _jolyTree_ and to describe its output files, the following use case example describes its usage for inferring an exploratory phylogenetic tree of _Klebsiella_ genomes.
In order to illustrate the usefulness of _JolyTree_ and to describe its output files, the following use case example describes its usage for inferring a phylogenetic tree of _Klebsiella_ genomes derived from the analysis of [Rodrigues et al. (2019)](https://doi.org/10.1016/j.resmic.2019.02.003).
##### Downloading genome sequences
The following command lines allows downloading the genome sequences of 39 _Klebsiella_ species from the [NCBI genome repository](https://www.ncbi.nlm.nih.gov/genome) inside a directory named _genomes_:
The following [Bash](https://www.gnu.org/software/bash/)command lines allows the genome sequences of 40 _Klebsiella_ species (36 belonging to the _Klebsiella pneumoniae_ complex –Kp1 to Kp7– and 4 outgroup species –Kog–) to be downloaded from the [NCBI genome repository](https://www.ncbi.nlm.nih.gov/genome) inside a directory named _genomes_:
while read-r s a;do echo$t.$s;([[$a=~ $A1]]&&$EUTILS$a||$NCBIFTP${a:0:2}/${a:2:2}/$([[$a=~ $A2]]&&echo${a:4:2}/)$a/$a$Z|zcat)>genomes/$t.$s.fa;done
```
##### Launching _jolyTree_
...
...
@@ -205,6 +202,8 @@ Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University P
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM (2016) Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology, 17(1):132. [doi:10.1186/s13059-016-0997-x](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x).
Rodrigues C, Passet V, Rakotondrasoa A, Abdoulaye Diallo T, Criscuolo A, Brisse S (2019) Description of _Klebsiella africanensis_ sp. nov., _Klebsiella variicola_ subsp. _tropicalensis_ subsp. nov. and _Klebsiella variicola_ subsp. _variicola_ subsp. nov. Research in Microbiology. [doi:10.1016/j.resmic.2019.02.003](https://doi.org/10.1016/j.resmic.2019.02.003).
Tajima F, Nei M (1982) Biases of the estimates of DNA divergence obtained by the restriction enzyme technique. Journal of Molecular Evolution, 18(2):115-120. [doi:10.1007/BF01810830](https://link.springer.com/article/10.1007/BF01810830).
Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution, 1(3):269-285. [doi:10.1093/oxfordjournals.molbev.a040317](https://academic.oup.com/mbe/article/1/3/269/1244029).
