HTML Report

Concept

This align module generates several sets of alignments that are ready-to-use in popular phylogenetic tree inference programs (e.g., IQ-TREE, RAxML, ASTRAL). Each alignment set differs from one another in the following four respects: 1) whether they are trimmed, 2) which paralog filter is applied, 3) whether they contain reference sequences, and 4) in which formats . Thus, it is important to understand the differences between each alignment set and carefully evaluate their quality in order to decide which alignment set to use for subsequent analyses.

Open the report captus-assembly_align.report.html with your browser (internet connection required) to explore and compare general alignment statistics for each locus and each sample!

Tips

Contents

1. Stats Comparison at Each Processing Step

This plot shows distributions of general alignment statistics at each processing step.

Features:

  • Switch the Marker Type dropdown to change the marker type
    (appeared only when you have more than one marker type).
  • Switch the dropdown on the x-axis to change the variable to show.
  • Click on the legend to toggle hide/show of each format.

Depending on --filter_method argument, you will have up to 12 processing steps as follows:

Processing step (Path to alignments) Trimmed Paralog filter With references
02_untrimmed/01_unfiltered_w_refs No None Yes
02_untrimmed/02_naive_w_refs No Naive Yes
02_untrimmed/03_informed_w_refs No Informed Yes
02_untrimmed/01_unfiltered No None No
02_untrimmed/02_naive No Naive No
02_untrimmed/03_informed No Informed No
03_trimmed/01_unfiltered_w_refs Yes None Yes
03_trimmed/02_naive_w_refs Yes Naive Yes
03_trimmed/03_informed_w_refs Yes Informed Yes
03_trimmed/01_unfiltered Yes None No
03_trimmed/02_naive Yes Naive No
03_trimmed/03_informed Yes Informed No

For more explanations, read Output Files.

Variable Description Unit
Sequences Number of sequences in the alignment -
Samples Number of samples in the alignment -
Sequences Per Sample = Sequences / Samples -
Alignment Length Length of the alignment aa/bp
Informative Sites Number of parsimony-informative sites that have at least two different characters and at least two of which appear in at least two sequences -
Informativeness = (Informative Sites / Alignment Length) * 100 %
Uninformative Sites = Alignment Length - Informative Sites
= Constant Sites + Singleton Sites		 -
Constant Sites Number of invariant sites in the alignment -
Singleton Sites Number of variable sites where one character appears in multiple sequences while other characters appear in only one sequence -
Patterns Number of unique sites that have different character configurations -
Mean Pairwise Identity Mean pairwise sequence identity in the alignment %
Missingness Proportion of -, N, X, ?, ., and ~ in the alignment %
GC Content GC content of the alignment (inapplicable to AA format) %
GC Content at 1st Codon Position GC content at 1st codon position in the alignment
(only applicable to NT format)		 %
GC Content at 2nd Codon Position GC content at 2nd codon position in the alignment
(only applicable to NT format)		 %
GC Content at 3rd Codon Position GC content at 3rd codon position in the alignment
(only applicable to NT format)		 %

For more explanation about sites and patterns, see IQ-TREE’s FAQ: What are the differences between alignment columns/sites and patterns?

2. Bivariate Relationships and Distributions

This plot shows general alignment statistics for each alignment (locus).
When your result contains more than one marker type, the report will include separate plots for each marker type.

Features:

  • Switch the Processing Step dropdown to change the processing step to show the statistics.
  • Switch the dropdowns on the x- and y- axes to change variables to plot on each axis.
  • Click on the legend to toggle hide/show of each format.

Depending on --filter_method argument, you will have up to 12 processing steps as follows:

Processing step (Path to alignments) Trimmed Paralog filter With references
02_untrimmed/01_unfiltered_w_refs No None Yes
02_untrimmed/02_naive_w_refs No Naive Yes
02_untrimmed/03_informed_w_refs No Informed Yes
02_untrimmed/01_unfiltered No None No
02_untrimmed/02_naive No Naive No
02_untrimmed/03_informed No Informed No
03_trimmed/01_unfiltered_w_refs Yes None Yes
03_trimmed/02_naive_w_refs Yes Naive Yes
03_trimmed/03_informed_w_refs Yes Informed Yes
03_trimmed/01_unfiltered Yes None No
03_trimmed/02_naive Yes Naive No
03_trimmed/03_informed Yes Informed No

For more explanations, read Output Files.

Variable Description Unit
Sequences Number of sequences in the alignment -
Samples Number of samples in the alignment -
Sequences Per Sample = Sequences / Samples -
Alignment Length Length of the alignment aa/bp
Informative Sites Number of parsimony-informative sites that have at least two different characters and at least two of which appear in at least two sequences -
Informativeness = (Informative Sites / Alignment Length) * 100 %
Uninformative Sites = Alignment Length - Informative Sites
= Constant Sites + Singleton Sites		 -
Constant Sites Number of invariant sites in the alignment -
Singleton Sites Number of variable sites where one character appears in multiple sequences while other characters appear in only one sequence -
Patterns Number of unique sites that have different character configurations -
Mean Pairwise Identity Mean pairwise sequence identity in the alignment %
Missingness Proportion of -, N, X, ?, ., and ~ in the alignment %
GC Content GC content of the alignment (inapplicable to AA format) %
GC Content at 1st Codon Position GC content at 1st codon position in the alignment
(only applicable to NT format)		 %
GC Content at 2nd Codon Position GC content at 2nd codon position in the alignment
(only applicable to NT format)		 %
GC Content at 3rd Codon Position GC content at 3rd codon position in the alignment
(only applicable to NT format)		 %

For more explanation about sites and patterns, see IQ-TREE’s FAQ: What are the differences between alignment columns/sites and patterns?

3. Stats Per Sample

This plot shows general alignment statistics for each sample.
When your result contains more than one marker type, the report will include separate plots for each marker type.

Features:

  • Switch the Sort Samples by dropdown to re-sort the x-axis by sample name or mean of the variable.
  • Switch the dropdown on the y-axis to change the variable to show.
  • Click on the legend to toggle hide/show of each data series.

Variable Description Unit
Number of Loci Number of alignments (loci) containing the sample -
Mean Ungapped Length Mean sequence length of the sample excluding gaps (-) aa/bp
Total Ungapped Length Cumulative sequence length of the sample excluding gaps (-) aa/bp
Mean Gaps Mean length of internal gaps (-) -
Total Gaps Cumulative length of internal gaps (-) -
Mean Ambiguities Mean count of ambiguous characters of the sample -
Mean GC Content Mean GC content of the sample (inapplicable to AA format) %
Mean GC Content at 1st Codon Position Mean GC content at 1st codon position of the sample (only applicable to NT format) %
Mean GC Content at 2nd Codon Position Mean GC content at 2nd codon position of the sample (only applicable to NT format) %
Mean GC Content at 3rd Codon Position Mean GC content at 3rd codon position of the sample (only applicable to NT format) %
Mean Copies Mean number of sequences per alignment (always 1 for alignments with paralog filter applied) %

Created by Gentaro Shigita (11.08.2021)
Last modified by Gentaro Shigita (17.10.2022)