Comments (6)
from muscle.
The maximum length was 2868 aa, would that be too long?
from muscle.
Could be, I can check if you post the sequences. What are the sequences? Can't you trim them to a globally alignable region? The length variation is pretty big to get a good MSA from any algorithm.
from muscle.
These are representative tRNA synthetases from across the tree of life, but I need the alignment to construct a phylogenetic tree.
sequences.txt
from muscle.
The memory allocation fails because the alignment exceeds 50,000 columns at an intermediate step. The final alignment would probably have far more columns. These sequences are too far diverged to make a reasonable alignment, there is no chance of building a good tree from them.
from muscle.
Thanks for the responses, just wanted to update we've narrowed the study down to a specific domain with less length variation and muscle works for us now!
from muscle.
Related Issues (20)
- Resampling Clarification HOT 5
- Can muscle be made to take two or more non-file cli arguments (input streams)? [v3.8] HOT 1
- gap penlty HOT 2
- @ in output filename required for -perm all with -super5 HOT 1
- Memory Object Too Large due to very long sequences HOT 2
- Automatic optimal number of threads HOT 2
- If is possible to release Muscle V5 version which has no dependence of omp.h? HOT 8
- Specifying threads HOT 4
- usorter.cpp(88) assert failed: L >= m_WordLength HOT 2
- Segmentation fault (core dumped)riors HOT 2
- Segmentation fault : only a few small sequences to align HOT 1
- alignment error when short sequence HOT 5
- Running time for large numbers of sequences
- python version of the code? HOT 1
- Fatal error: allocflat.cpp(15) assert failed: uint64(Size) == Size64 HOT 1
- segmentation fault muscle -align testing.fa -output alignment.afa HOT 3
- Error in `muscle': free(): invalid next size (normal): 0x00002b09305f4a40 ***
- How can I download v5 muscle? HOT 5
- 2 nts are "cut" from the rest. HOT 2
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from muscle.