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CDS length in C. reinhardtii genes was positively correlated with both Δ L (ρ = 0.393, P < 10−) and UnalignRes regardless of alignment tool used (ClustalW: ρ = 0.412, P < 10−; MUSCLE: ρ = 0.481, P < 10−), indicating in general there was better alignment for orthologs encoding shorter proteins.
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He says that the overall vision is "better alignment between corporate strategies and the people who actually have to execute those strategies on the front line".
A second reason for the better performance of informativeness predictions for amino acid sequences could be better alignment.
Inspection of the alignment and comparisons to similar alignments produced using CLUSTALW [ 16] showed that the MUSCLE alignment was better at correctly aligning the zinc coordinating amino acids and fewer manual adjustments were required than with CLUSTALW results (data not shown).
Alignments for reads for which the new alignment, if any, was better than the original BWA alignment were changed.
Alignment accuracy was better at lower concentrations of α-factor (∼10 nM), but significant orientation occurred over a broad range of α-factor concentrations.
We find that local alignments are better than multiple alignments for a detailed match of the TFBSs and for the identification of functional elements in orthologous sequences.
Newly developed tools for (multiple) sequence alignment are more dynamic, using adjustable local algorithms and instant global replotting, and as such are better suited for alignment of distantly related sequences [44], [45].
TM-align, for instance, is particularly robust in quantifying comparisons between sets of proteins with great disparities in sequence lengths, but it only indirectly captures hydrogen bonding or secondary structure order conservation which might be better metrics for alignment of evolutionarily related proteins.
A relaxed selection of blocks is better for short alignment [54], thus the settings were the following for the 18S rDNA [1: 12; 2: 17; 3: 4; 4: 3; 5: all] and 28S rDNA [1: 11; 2: 11; 3: 4; 4: 4; 5: all].
If the score of a new alignment by a thread is better than the original alignment, then it instantly replaces the original alignment.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com