Last updated: 2021-03-18
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Knit directory: wildlife-haemoprotozoa/
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| Rmd | d429fdd | siobhon-egan | 2021-03-18 | First publish |
Alignment using muscle (default parameters), trimmed and then refined using muscle refine alignment option.
Maximum likelihood analysis using IQTREE.
Load data
piroiq <- read.iqtree("data/Sanger-piroplasm/IQ-TREE-210212103834/muscle_aln_860bp_refined.fasta.treefile") # load IQTREE output
pironx <- read.newick("data/Sanger-piroplasm/IQ-TREE-210212103834/HXFe4hqem8tiVAHc8-bIwg_newick.newick") # load IQTREE output
metadata_tree <- read_csv("data/Sanger-piroplasm/pirobloods.csv")ggtree(pironk) + geom_text(aes(label = label)) ggtree(piroiq) + geom_text(aes(label=node), hjust=-.3) ggtree(pironk) + geom_tiplab() tre.new <- rotate(pironk, c(58, 56))
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] phangorn_2.5.5 ape_5.4-1 ggrepel_0.9.1 ggstar_1.0.1
[5] ggtreeExtra_1.0.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4
[9] purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.1.0
[13] ggplot2_3.3.3 tidyverse_1.3.0 treeio_1.14.3 ggtree_2.4.1
[17] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] httr_1.4.2 sass_0.3.1 jsonlite_1.7.2
[4] modelr_0.1.8 bslib_0.2.4.9001 assertthat_0.2.1
[7] BiocManager_1.30.10 rvcheck_0.1.8 cellranger_1.1.0
[10] yaml_2.2.1 pillar_1.5.0 backports_1.2.1
[13] lattice_0.20-41 quadprog_1.5-8 glue_1.4.2
[16] digest_0.6.27 promises_1.2.0.1 rvest_0.3.6
[19] colorspace_2.0-0 htmltools_0.5.1.1 httpuv_1.5.5
[22] Matrix_1.3-2 ggnewscale_0.4.5 pkgconfig_2.0.3
[25] broom_0.7.5 haven_2.3.1 patchwork_1.1.1
[28] tidytree_0.3.3 scales_1.1.1 whisker_0.4
[31] later_1.1.0.1 git2r_0.28.0 generics_0.1.0
[34] ellipsis_0.3.1 withr_2.4.1 lazyeval_0.2.2
[37] cli_2.3.1 magrittr_2.0.1 crayon_1.4.1
[40] readxl_1.3.1 evaluate_0.14 fs_1.5.0
[43] fansi_0.4.2 nlme_3.1-152 xml2_1.3.2
[46] tools_4.0.3 hms_1.0.0 lifecycle_1.0.0
[49] aplot_0.0.6 munsell_0.5.0 reprex_1.0.0
[52] compiler_4.0.3 jquerylib_0.1.3 rlang_0.4.10
[55] grid_4.0.3 rstudioapi_0.13 igraph_1.2.6
[58] rmarkdown_2.7.2 gtable_0.3.0 DBI_1.1.1
[61] R6_2.5.0 gridExtra_2.3 lubridate_1.7.10
[64] knitr_1.31 utf8_1.1.4 fastmatch_1.1-0
[67] rprojroot_2.0.2 stringi_1.5.3 parallel_4.0.3
[70] Rcpp_1.0.6 vctrs_0.3.6 dbplyr_2.1.0
[73] tidyselect_1.1.0 xfun_0.21