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| File | Version | Author | Date | Message |
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| html | 3fa8e62 | Maeva TECHER | 2024-11-09 | updated analysis |
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IMPORTANT
We used OrthoFinder results, PAL2NAL and HyPHY
to identify signatures of selection in 1:1 orthologous genes. For this
part, refers to the AMAZINGLY WELL CURATED pipeline FormicidaeMolecularEvolution
by Megan Barkdull
(PhD Student at Cornell University). We describe below the modifications
made and mostly copied the workflow from her Github.
The script written by M. Barkdull has not been changed but we have to
call R with phylotools installed first. This step ensures
to reorder the orthofinder fasta file so instead of being one file per
orthogroup, we will have one species file for all orthogroups together
and reordered.
ml GCC/12.2.0 OpenMPI/4.1.4 R_tamu/4.3.1
export R_LIBS=$SCRATCH/R_LIBS_USER/
./scripts/DataMSA.R ./scripts/inputurls_18polyneoptera_Nov2024.txt /scratch/group/songlab/maeva/LocustsGenomeEvolution/Version3/5_OrthoFinder/fasta/OrthoFinder/Results_Nov08/MultipleSequenceAlignments
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 15.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Asia/Tokyo
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.3 knitr_1.49 rlang_1.1.4
[5] xfun_0.49 stringi_1.8.4 promises_1.3.2 jsonlite_1.8.9
[9] workflowr_1.7.1 glue_1.8.0 rprojroot_2.0.4 git2r_0.35.0
[13] htmltools_0.5.8.1 httpuv_1.6.15 sass_0.4.9 fansi_1.0.6
[17] rmarkdown_2.29 jquerylib_0.1.4 evaluate_1.0.1 tibble_3.2.1
[21] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4 whisker_0.4.1
[25] stringr_1.5.1 compiler_4.4.1 fs_1.6.5 Rcpp_1.0.13-1
[29] pkgconfig_2.0.3 rstudioapi_0.17.1 later_1.4.1 digest_0.6.37
[33] R6_2.5.1 utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
[37] bslib_0.8.0 tools_4.4.1 cachem_1.1.0