MACSE
What it is
MACSE = Multiple Alignment of Coding SEquences It’s a specialized alignment tool designed specifically for coding sequences (CDS).
Why it exists
Standard aligners (MAFFT, Clustal) don’t understand codons. They may:
Introduce frameshifts
Break codons
Misalign stop codons
MACSE fixes this by aligning sequences codon‑aware, preserving reading frames
When you use it
Aligning viral ORFs (e.g., SVA VP1, SARS‑CoV‑2 Spike)
Preparing alignments for selection analysis (HyPhy, PAML)
Comparing coding regions across strains
Detecting frameshift mutations
Bowtie / Bowtie2
What it is
A fast read aligner used to map FASTQ reads to a reference genome.
What it does
Takes millions of short reads
Aligns them to a reference
Produces a SAM/BAM file
When you use it
Variant calling pipelines
RNA‑seq mapping
Metagenomics filtering
Viral read mapping
| Bowtie | Bowtie2 |
|---|---|
| Very fast | Fast |
| For short reads (≤50 bp) | For longer reads (100–300 bp) |
| Less sensitive | More sensitive |
Epi2ME
What it is
A cloud‑based analysis platform from Oxford Nanopore Technologies (ONT).
What it does
Runs ONT workflows such as:
Basecalling
Read QC
Taxonomic classification
Variant calling
AMR detection
Metagenomics
When you use it
If you have Nanopore sequencing data, Epi2ME gives you:
Push‑button analysis
Real‑time results
Cloud processing