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We should crop off these poorly aligned regions on the ends of the alignment before moving on.
Repeat this procedure for both ends of the alignment, if needed (you will need to select and scroll starting from the opposite end to do this).
The local similarity is observed at the ends of the alignment.
Long ends of the alignment were trimmed and a neighbor joining analysis was performed in PAUP* 4.0b.
RefAligner reports local alignments between two maps and applies a fixed penalty based on the user-defined likelihood of unaligned labels at the ends of the alignment.
Similar(55)
We chose unambiguously aligned regions, removing the ends of the alignments, and excluded CpG sites from the alignments.
Sometimes, regions at the beginning or end of the alignment will be poorly aligned because the sequences were too dissimilar in length.
Both Colubraria contigs appear to be incomplete, with comp1091011_c0_seq4 having a predicted signal peptide but missing the C-terminal tail and comp109011_c1_seq2 aligning with the C-terminal end of the alignment.
Phylogenetic analyses were performed using near full-length aligned SSU rDNA sequences, only the extreme 5'-and 3'-ends of the alignment were excluded leaving 1472 sites, using PHYLIP 3.6b [45].
At the end of the alignment (Panels A and B) a black line marks the end of the protein including the peptide.
The top row shows the results obtained when LRTs of the molecular clock were conducted in 14 windows by starting at positions 1 500, then moving in 500 bp steps (e.g., positions 1 500, 501 1000, etc)., until the end of the alignment was reached.
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CEO of Professional Science Editing for Scientists @ prosciediting.com