To still run Jalview with this error you will need to go to the Jalview website and run the desktop version of the program.
Clustal Omega uses a different method to calculate the guide tree compared to ClustalW, so we do not output the rough all-against-all pairwise alignment scores used to guide the alignment (as they don't exist). However we do calculate a pairwise identity matrix from the results, which can be downloaded from the Results Summary tab.
I'm gonna also agree, your camber so so far out of spec I suspect a bent housing. Caster that low would be indicative of improperly adjusted control arms or too high a lift for stock arms.
Caster is way too low. DO NOT USE CAM BOLTS!
Trick question! Multiple sequence alignment tools like Clustal Omega are designed to align three or more sequences. To align two sequences you should use our pairwise alignment tools: http://www.ebi.ac.uk/Tools/psa/
Clustal Omega is the latest tool from the Clustal authors. It aligns three or more sequences together in a computationally efficient and accurate manner.
The claimed spec for the cross camber is -0.3 to 0.8 and yours is slightly out of spec in terms of the overall difference between the front wheels even though both front wheels are in spec. So it may have a bit more of a tendency to pull to the left than if it were in spec.
Add a set of quality adjustable lower control arms.
The program accepts nucleic acid or protein sequences, in the following multiple sequence formats:
An * (asterisk) indicates positions which have a single, fully conserved residue. A : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix. A . (period) indicates conservation between groups of weakly similar properties - scoring =< 0.5 in the Gonnet PAM 250 matrix.
The tree image cannot be saved directly as it is a dynamic java-driven interface, however you can take a screenshot and then save this in an image editing program, or as mentioned above use the tree data to recreate the tree in another tree viewing program and save it from there.
Information about sequence formats can be found at the EMBOSS sequence formats guide. If you're not sure, try using FASTA format. You can also use tools like Readseq to convert between sequence formats.
Very long or badly aligning nucleotide sequences (so that the alignment approaches 100k characters in length) may cause Clustal Omega to fail.
Due to a security issue we will be resetting all users' passwords. This reset will be taking place between Tuesday June 21st - Thursday June 23rd.
Clustal Omega produces this error when it can't find the sequence data to go with a sequence identifier. This can happen if sequence data is missing from the input or the data is on the same line as the header - make sure the sequence data is on a new line.
The default output format (ALN/Clustal format) truncates sequence identifiers to 30 characters - this may also affect the ability of the job to run if the first 30 characters are not unique. The PHYLIP format truncates even more restrictively, to 10 characters. To prevent truncation change the output format to a type that does not have a limit, such as pearson/FASTA.
Yea more details like what kit, height. Do you have uppers too?
More help can be found in the help documentation (http://www.ebi.ac.uk/Tools/msa/clustalo/help/index.html). For specific help about any problems with or if you have any feedback on Clustal Omega at EMBL-EBI please feel free to contact our helpdesk (http://www.ebi.ac.uk/support/sequence-alignment) ideally including full details about your problem and the URL of the page you are contacting us about.
Results are stored at EMBL-EBI for a week from the date of job submission.
I just took my car to get it aligned and all numbers came back within standards, at least according to sheet given to me at the facility, with the exception of one: Cross Camber. I will try to add all numbers here for reference:
This occurs when something is wrong with your sequence input. It is often caused by using a sequence format not supported by Clustal Omega, or a problem with the formatting for example sequence data not being on a newline from the sequence header line. Clustal Omega requires sequences to be formatted, not just raw sequence data.
Something like this: https://www.allensoffroad.com/suspension-systems-lift-kits/Core-4X4-Control-Arms/Wrangler-TJ-1997-2006-Core4x4/Core4X4-TIER-THREE-JK/JK-2007-Present-Front-Lower-Adj-Control-Arm-Set-T3
Paste the sequences in an accepted format into the same box: Clustal Omega accepts multiple sequence formats as input - these formats allow for multiple sequences to be placed in the same file or input box, as they each contain ways for Clustal Omega to distinguish where new sequences start. It is important to use correctly formated sequences for this reason.
To update your version of Java go to the Java.com download page.
The alignment will be in the format you specified in the input section, or Clustal by default if you didn't specify anything. They are all text files, so can be opened in any text viewing program that can deal with unix text characters (end of line characters for example). In Windows you can use WordPad. More specialist tools are available to investigate alignments and allow you to mark them up with colours for example. Genedoc and Jalview are two such tools.
Jalview relies on Java, which requires that applications present correct certificates for security reasons. If the Jalview program doesn't have a currently valid certificate then it will be prevented from running and this error will remain until we recieve an update from the author.
How high are you lifted? What kind of off roading do you do? You might want to do a set of adjustable uppers as well to really dial in your front end.
The tree data is in the widely used Newick format, there are several online or standalone tree viewing programs available that can take this and recreate the tree from this data.
To view parameter settings for Clustal Omega click the 'More options' buttons. Clicking on the parameter name will take you to the relevant help information.
Please note raw sequence data (just the sequence with no recognised formatting) will not work with Clustal Omega. If using sequences from NCBI we recommend saving them as FASTA format first. Sequence format conversion tools are available at http://www.ebi.ac.uk/Tools/sfc/.
For the precise version number of Clustal Omega being run please go to the submission details tab from your job results.
Cross Camber is the difference is camber between two wheels. In this case your front wheels. If both wheels are set the same, the cross camber zero. In your case the front left camber is -1.0 and the front right is -0.6.
This happens when we can't find the job that you have requested. Normally it's a result of trying to look at the page over a week after the job was submitted, so the data is no longer available at EMBL-EBI. If you've copied the URL from a recent email job, check for any mistakes in the link.
** (Note here how the actual worsened from the Before...Is this OK??),
Help with Alignment Numbers
Your caster is way low. I'm guessing your JK steering feels flighty at highway speeds. Ideally, you'd like your caster to be in the 4.2-4.5 range.
Clustal Omega needs unique sequence identifiers, which it defines as the first word on the sequence identifier line. Check that you've not got a duplicate identifier somewhere in the input, that you're not using spaces or tabs in your identifiers, and that the first 30 characters of your identifier are unique if using Clustal format files.
Clustal Omega produces several outputs, depending on the options you selected when submitting the job. By default the main output is the alignment file. A simple phylogenetic tree (via neighbour joining) can be found in the Phylogenetic Tree tab. A pairwise identity scores matrix and other outputs can be viewed/downloaded in the Results Summary tab.
This error sometimes occurs if you try to upload a really large input to our tools, far in excess of the limits described above. Make sure your input falls within the previously described limits.
Call around and find a local Jeep shop that has experience doing alignments with adjustable control arms and have them do the alignment. With adjustable arms there is no need for cam bolts.
By default, Clustal Omega outputs Clustal format alignments without numbering, to change this simply click 'more options' and change the output alignment format to 'Clustal w/ numbers'.