Mega X Alignment Download
Charise Zelnick
I observed a lot of gaps after the alignment, would it be better if I manually remove it or should I just retain it? I would also appreciate it if you'll leave me some tips or guide on how to trim gaps in the aligned sequences.
In MSA, gaps are introduced f.e. if one or some of the sequences have different lengths, insertions, etc. Gaps are normal to have to some extent. Eg. if one sequences contains a novel protein domain that the others do not, then all other sequences have gaps in these columns. Also, if the sequences are of different lengths, there will likely be gaps at the ends. First thing to do is check that your sequences are correct, especially if you are aligning DNA. Did you get the cDNA sequences right or do some contain intronic sequences? If introns are retained, try to remove them, or if you cannot get a correct cDNA, remove the whole sequence. You can consider to remove single sequences that cause extra many or large gaps anyway, they might be outliers and you might be able to reduce the number of gaps.
The good thing with MEGA is, you can simply try it out interactively. I suspect that gaps affect simpler methods like upgma, neighbor-joining, and parsimony, whereas more state-of-the-art methods like ML and Bayesian will be more robust. There, in my experience it is better to simply leave the alignment alone.
There is also the down-side of MEGA, which is that it doesn't contain much state-of-the-art methods. Stand-alone aligners like MAFFT and T-Coffee are possibly superior to Muscle at least in some cases and some settings, and specifically IQ-tree, RaXML, MrBayes, etc. are more exact and often much faster compared to the stuff that is built in MEGA. So I would recommend to try things out in MEGA but then use some advanced tools to try to get the optimal phylogeny.
Every case is likely going to be different and unfortunately may require a lot of trial and error to tune.
I tried to construct NJ tree, wherein I left the alignment alone. However, upon observation, I got bootstrap value lower than 70 in some nodes. I would like to ask if this is okay or should I attempt for a higher bootstrap value?
NJ is only for doing a quick initial screen, or initial tree generation for ML, but not for the final analysis, it was maybe ok 20 years ago before the more advanced methods were around or the computational power was limited. My recomendation is to try IQtree with at least 1000 ultra-fast bootstrap iterations and let it determine the optimal substitution model. BS values below 70% are common I think, anyway they might vary widely depending on the method and substitution matrix.
I have a set of GABA-edited data from the MEGA-sLASER sequence that I am trying to pre-process using Osprey. However, the alignment is way off (see images below). Any ideas as to why this is happening? From what I understand, for GABA-edited MEGA data, Osprey uses the residual water signal for alignment. Is there a way that I can specify a different peak for the alignment of these data (3.0 ppm, for example)?
Thanks for reporting this issue. Osprey is performing the alignment in the time-domain by optimizing the individual frequency and phase shifts of the transients compared to the transient with the highest similarity (Robust Correction of Frequency and Phase Errors in Edited MRS Data, Mikkelsen et al. 2018, ISMRM Proceedings).
The initial guess of this fit is based on the cross-correlation of groups of 10% of the transients with two delta functions at 3.01 and 3.22 ppm.
As for the LCModel basis set, I just updated my folders to most recent update in the develop branch. I was able to import the basis file into the Osprey format using the io_LCMBasis function. I used this new file for the fitting and it worked! I just had to add an if statement for the Siemens case in osp_fitInitialise, so that it would load the correct basis set.
The error in the scatter plot is a known issue which is haunting me for a long time :). The problem is that SPM12 fieldtrip toolbox includes functions with the same names as MATLAB internal functions. For that reason, I was moving SPM12 in and out of the path during the use of Osprey. I have now added a fix, which is just removing the filedtrip folder at Osprey startup. This seems to work in our testing framework.
During my last update I accidentally uploaded my SPMpath.mat variable on GitHub and removed it later. I suspect that you have downloaded the repository when it was still online. I have added a fix to avoid this bug in the future.
I updated the repository and now I am getting an error Undefined function or variable 'spm'. on the segmentation module. For some reason the spm path is removed either after coregistration or when I try to do the segmentation.
I could integrate a frequency restricted spectral feature into Osprey. If we agree on that I would appreciate to be considered in a potential manuscript, as this project would go beyond normal bug fixing.
Sorry to disturb you, given that this is a post from nearly 3 years ago. I am currently encountering a similar issue and came across this post. May I ask how you eventually resolved the issue of spectral alignment?
3.RestrSpecReg,with the fit range [0.5 4]
RestrSpecReg15461034 193 KB
It appears that ProbSpecReg performs better than the other two methods, although it is not optimal. Additionally, I noticed that my Cr peak is at 2.98 ppm rather than 3.02 ppm, and it shows a decreasing trend as the average increases.
I have been really struggling with getting my camera alignment situated. I have a FoxAlien Reizer mega which has a working area of 800mm long and 400mm high. I have the 8MP x 120 Degree camera from your site and have mounted it about 22 inches above my laser bed. When I run the alignment from the software, using an 5mm piece of wood and at 195% scale it fits on my workbed. After I mark the box it will only offer me a zoomed in image of the workbed in my working area even though the live picture shows the entirety of my enclosure that I have built. How can I get my camera and software to recognize that my work area is the full extent of the 800mmx400mm? I have run the camera calibration and used the presets for the lightburn camera. I am desperate to get the image perfect as I need to print on both sides of a material and use the second side to actually cut the material out and am unable to get the alignment perfect.
I was told, for the most accurate Print and Cut results put the registration marks as far apart as possible, jog toward the registration mark then pulse the CO2 laser and destructively approach the registration marks with perfect tiny dots.
After I mark the box it will only offer me a zoomed in image of the workbed in my working area even though the live picture shows the entirety of my enclosure that I have built. How can I get my camera and software to recognize that my work area is the full extent of the 800mmx400mm?
I apologize that it took so long to get back to this thread. The art is not an issue when it comes to the size of the work area. It is that the camera, while showing the entirety of the work area in live view, when I capture the background it only shows the area that was within the square made by the alignment calibration area and a little more. I made sure to enlarge the alignment of the square to the biggest possible area without leaving my actual working area (which is 195% the standard size), as when I try the standard size I lose even more of my work area than usual. I have checked the settings and use custom camera system is already selected. At the request of the email I sent to Lightburn proper I checked to make sure that the work area was in fact designated as the 400mm tall by 800mm wide. At one point, a few versions of Lightburn ago, I did not have this issue but that was multiple updates previously and I do not recall the build version that worked. I have tried making the reference points for the alignment calibration a rectangle to match the bed size and all that did was compress the background into a square instead of the work area proper. Sadly I am at my troubleshooting limits, even though my day job is IT.
I have an alignment of some full genome sequences of DENV1 that we have recently sequenced from the serum of patients. I have already cleaned the sequences, built the alignments and done the SNPs calling. After that I got the consensus sequences from each sample and I used MEGA to build the alignments of the consensus sequences and to construct a tree etc.
Now at the menu "Data" select "Export data"; at the "Sequence data export options window" if necessary select the data format again, and select "For each site" at "Writing site numbers", and select "Only highlighted sites" at "Selected sites to include".
Edit: I noticed the mega menu is aligned correctly to the left of the menu item when the main nav is aligned left. However, I need the main nav aligned right, but I still want the mega menu aligned to the left of menu item. Is this possible?
The Alignment of the Megamenu gets dependent on the Horizontal Menu Position of Nav Menu when the position of the Megamenu is set to Relative. So, When the Nav Menu position is set to Right the Megamenu will be left-aligned Since the Relative Position will display relative to its parent and also to itself. You can check this screencasting I made for you which will clarify it more.
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