Multiple alignment program for amino acid or nucleotide sequences

Input:
Paste sequences (<? nt. × <? sequences; original strands from the sequencer) in FASTA or FASTQ format.  Example

If the input data has both forward and reverse strands, they'll be automatically flipped as necessary.  Don't manually flip sequences in the input, in order to appropriately consider different error patterns between forward and reverse strands. 

Or, upload the input sequences as a plain text file (example)
or a .zip file containing a single plain text file (example):

UPPERCASE / lowercase:

Same as input (unavailable)

Forward strand → UPPERCASE / Reverse strand → lowercase

Output order:

Same as input

Aligned

Job name (optional; used as output file name and subject of emails):

(basic Latin alphabet, number and space only)

Notify when finished (optional; recommended when submitting large data):

Email address:

Strategy:
For partially overlapping data:

o-o------- -oooo----- ---o-ooo-- -------ooo

lamassemble 🦙   The output does not always include all input sequences.

Fast

Accurate; -z 1000 -m 2×(number of sequences)

For fully overlapping data:

o-oooo--oo oooo-ooo-- -ooo---ooo ooo-----oo

MAFFT with parameters estimated by LAST-TRAIN:

Auto (FFT-NS-1, FFT-NS-2, FFT-NS-i or L-INS-i; depends on data size) 

FFT-NS-1 (for less than 100,000 sequences shorter than 50,000 sites (?))

FFT-NS-2 (for less than 100,000 sequences shorter than 50,000 sites (?))

G-large-INS-1 (for less than 10,000 sequences shorter than 5,000 sites)

G-large-INS-1 (for less than 100,000 sequences shorter than 5,000 sites; MPI)

L-large-INS-1 (for less than 10,000 sequences shorter than 5,000 sites)

L-large-INS-1 (for less than 100,000 sequences shorter than 5,000 sites; MPI)

G-INS-i (for less than 1,000 sequences shorter than 5,000 sites)

L-INS-i (for less than 1,000 sequences shorter than 5,000 sites)

Parameters:

Estimate from input data   New! 2023/Nov

Number of iterative training: 1 3 5

Estimated from human DNA sequenced with PromethION R9.4, base-called with Guppy 1.4.0 (De Coster et al. 2019, ERR2631604)
Examples for lamassemble  for mafft

Estimated from human RNA (direct RNA), sequenced with PromethION R9.4, base-called with Albacore
Examples for lamassemble  for mafft

Estimated from human DNA sequenced with PacBio Sequel II, Continuous Long Reads (Wenger et al. 2019, SRR9972588)
Examples for lamassemble  for mafft

Preset for Pacbio / ... CCS ... (Wenger et al. 2019, SRX5327410)
Examples for lamassemble  for mafft

User-defined parameter file (example):

Use pairwisely aligned sites by LAST (for partially overlapping data):

Error probability of: < 1e-5 < 1e-3 < 2e-3 < 0.01 < 0.1

Plot LAST hits (DNA only):

The top sequence vs the others     The longest sequence vs the others

Plot and alignment     Plot only     Alignment only

Threshold: score=39 (E=8.4e-11) score=22 (E=0.00805) score=20 (E=0.0699) score=12 (E=398)

Memory usage:

Normal mode