CrocoPhylogeny
Web-based phylogenetic analysis of whole genomes and complex sequences in just three clicks
To help in prioritizing the research and development of new and effective antibiotics treatments, the World Health Organization recently issued a global priority list of antibiotic-resistant bacteria considered to have the most substantial impact on global health at the current time. Whereas the phylogeny of prokaryotes is often judged based only on the 16S ribosomal RNA gene such relationships do not coincide with those based on various antibiotic resistance genes. Furthermore, the genetic basis of antibiotic resistance is not fully understood in all these pathogens. Therefore, it is of interest to examine the phylogeny of high-priority bacterial pathogens across their entire genomes. The taxonomic classification of the species of origin is included for comparison.
The settings for this case study were:
Forward only / Forward and reverse: Forward only
Speed/sensitivity: sensitive
Length of subsequence: 160
| Quality/score filter* | Distance matrix file MAX | Distance matrix file MIN | Neighbor Joining tree MAX | Neighbor Joining tree MIN | Visualize tree in iTOL MAX | Visualize tree in iTOL MIN |
|---|---|---|---|---|---|---|
| 16 | Matrix_MAX_Q16 | Matrix_MIN_Q16 | NJ_tree_MAX_Q16 | NJ_tree_MIN_Q16 | iTOL visualization of NJ_tree_MAX_Q16 | iTOL visualization of NJ_tree_MIN_Q16 |
| 22 | Matrix_MAX_Q22 | Matrix_MIN_Q22 | NJ_tree_MAX_Q22 | NJ_tree_MIN_Q22 | iTOL visualization of NJ_tree_MAX_Q22 | iTOL visualization of NJ_tree_MIN_Q22 |
| 28 | Matrix_MAX_Q28 | Matrix_MIN_Q28 | NJ_tree_MAX_Q28 | NJ_tree_MIN_Q28 | iTOL visualization of NJ_tree_MAX_Q28 | iTOL visualization of NJ_tree_MIN_Q28 |
| 34 | Matrix_MAX_Q34 | Matrix_MIN_Q34 | NJ_tree_MAX_Q34 | NJ_tree_MIN_Q34 | iTOL visualization of NJ_tree_MAX_Q34 | iTOL visualization of NJ_tree_MIN_Q34 |
| 40 | Matrix_MAX_Q40 | Matrix_MIN_Q40 | NJ_tree_MAX_Q40 | NJ_tree_MIN_Q40 | iTOL visualization of NJ_tree_MAX_Q40 | iTOL visualization of NJ_tree_MIN_Q40 |
If you experience issues while trying to visualize the trees in iTOL (e.g., iTOL server is down, link does not work, etc.), you can visualize your tree files online at T-REX or IcyTree.
* scores are calculated identically to those of BLAST+ (gap opening penalty = -5; gap extension penalty = -2; nucleic match = 1; nucleic mismatch = -3).
Higher quality/score filter indicates a higher minimal threshold for aligned subsequences to be considered when generating the average similarity score between two sequences (for details on the score filters please check our user manual).
Download all results as a zip file* scores are calculated identically to those of BLAST+ (gap opening penalty = -5; gap extension penalty = -2; nucleic match = 1; nucleic mismatch = -3).
Higher quality/score filter indicates a higher minimal threshold for aligned subsequences to be considered when generating the average similarity score between two sequences (for details on the score filters please check our user manual).
Representative tree
Service version 1.0.18.12.23 (change log).