CrocoPhylogeny
Web-based phylogenetic analysis of whole genomes and complex sequences in just three clicks
The Y chromosome is primarily responsible for sex determination but also carries other genes. However, the Y chromosome is an enigmatic part of the genome. For example, in humans, the Y chromosome is approximately 60 million bp in length but carries less than 100 protein-coding genes. For comparison, the X chromosome is only 2.5 times bigger (approximately 150 million bp in length) but carries almost 10 times more protein-coding genes (almost 900). Moreover, the Y chromosome is severely degenerated, with some scholars suggesting it might even be going extinct. Studies of the Y chromosome typically examine very small and highly conserved parts such as gene coding sequences. It is therefore interesting to examine the phylogeny of mammalian Y chromosomes across the entire sequence. 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 and reverse
Speed/sensitivity: sensitive
Length of subsequence: 320
| 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).