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

The entire report is based on data stored in the following two files:
- captus-assembly_align.alignments.tsv
- captus-assembly_align.samples.tsv
All tables and plots in the report are interactive powered by Plotly.
Visit the following sites once to take full advantage of its interactivity:
- https://plotly.com/chart-studio-help/getting-to-know-the-plotly-modebar
- https://plotly.com/chart-studio-help/zoom-pan-hover-controls

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.

Description of each processing step

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

Description of each variable

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)	%

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.

Description of each processing step

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

Description of each variable

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)	%

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.

Description of each variable

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)

HTML Report

Concept

Contents

1. Stats Comparison at Each Processing Step

2. Bivariate Relationships and Distributions

3. Stats Per Sample