Tempest For Mac
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For this tutorial, the Mac OS X version will be shown but the Linux & Windows versions will have exactly the same layout and functionality. When started, TempEst will immediately display a file selection dialog box in which you can select the tree that you made in the previous section. Select iceviruses.fasta.treefile and click Open. When we created Tempest, we focused on the most thrilling part of pirate life – sea battles. As you navigate the dangerous waters of the game you won’t just catch up with merchants, but you will encounter fellow pirates, creepy followers of a mysterious cult and terrible mythical monsters: Kraken, Leviathan and other infamous creatures. Tempest is a Pirate Open World Action RPG where you rove the seas across three continents filled with dozens of colonies and forts, hundreds of quests and countless ships to plunder. Customize your ship, trade, challenge fellow pirates and face terrible mythical monsters such as Kraken and Leviathan. The Tempest KIRIN. Named after a mythological beast from East Asian folklore known for its swiftness and grace, Tempest wants to invoke a feeling of speed and fluidity whenever you use this keyboard. Ultra Durable Shine Resistant PBT Keycaps. Give us a call at (682)477-4220 to reserve your spot in class! Please make sure you fill out a waiver here first for the location you are interested in.
*Tempest For Clarinet
*Tempest Form A And B
*Tempest For Mac Wallpaper
*Tempest For Mac
*Tempest Form A Instruction GuideThis tutorial describes the use of TempEst to examine the temporal signal of a data set and to look for problematic or erroneous sequences.
In this tutorial, we will explore the use of the interactive graphical program TempEst (formerly known as Path-O-Gen) to examine virus sequence data that has been sampled through time to look for problematic sequences and to explore the degree and pattern of temporal signal. This can be a useful way of examining the data for potential issues before committing significant time to running BEAST.Building a non-molecular clock tree
To examine the relationship between genetic divergence and time (temporal signal), we require a phylogenetic tree constructed without assuming a molecular clock. There is a wide range of suitable software packages (i.e., PhyML, RAxML, GARLI) but for this tutorial we are going to use IQ-Tree which uses a fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.The data for this tutorial was compiled for this paper: Worobey (2009) Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus. Journal of Virology, 82, 3769–3774. DOI: 10.1128/JVI.02207-07. This was a response to an earlier paper (Zhang et al (2006) J Virol80, 12229–12235 DOI: 10.1128/JVI.00986-06 ) which claimed to have isolated and sequenced influenza viruses from glacial ice.
You can download the file, ice_viruses.fasta, here.
Install IQ-Tree using the instructions on the website and open a command-line prompt, navigating to the directory containing the data file ice_viruses.fasta.
To build a maximum likelihood phylogenetic tree using the GTR+gamma model type:
This will create a set of files in the directory containing various outputs and results:
Join 25 million people and teams who organize, plan, and collaborate on tasks and projects with Any.do. “Best to-do list app” by the WSJ. The best calendar app for life & work. Control your day, week and month with calendar events and tasks in a single view. It’s the best way to manage your time and achieve your ambitious goals. Anydo for macbook air.
For our purposes we only need the maximum likelihood tree file ice_viruses.fasta.treefile. You can delete the other files if you like.Running TempEst and loading the treeRun TempEst by double clicking on its icon. TempEst is an interactive graphical application for examining the temporal signal in a tree of time-stamped sequences by plotting the divergence of each tip from the root against the date of sampling (a root-to-tip plot).
Once running, TempEst will look similar irrespective of which computer system it is running on. For this tutorial, the Mac OS X version will be shown but the Linux & Windows versions will have exactly the same layout and functionality.
When started, TempEst will immediately display a file selection dialog box in which you can select the tree that you made in the previous section.
Select ice_viruses.fasta.treefile and click Open.Parsing dates of sampling
Once the tree is loaded the main window will appear and look like this:
Ignore the panel on the left for the moment. The first thing that needs doing is to give the date of sampling to each of the sequences.
The actual year of sampling is given at the end of the name of each taxon. To specify the dates of the sequences in BEAUti we will use the Parse Dates button at the top of the panel. Clicking this will make a dialog box appear:Tempest For Clarinet
This operation attempts to extract the dates from the taxon names. It works by trying to find a numerical field within each name. This dialog box is the same as that in BEAUti and there are a wide range of options for doing this - See this page for details about the various options for setting dates in this panel. For these sequences you can set the options to look like the figure above: Defined just by its order, Order: last and Parse as a number option.
When parsing a number, you can ask BEAUti to add a fixed value to each date which can be useful for transforming a 2 digit year into a 4 digit year. Because all dates are specified in a four digit format in this case, no additional settings are needed. So, we can press OK.
The table will now have the year of sampling for each virus in the Dates column. Click on the Dates column header to sort the dates and check that they are all correct.The temporal signal and rooting
We can now explore the data using the tabs at the top of the window - Tree, Root-to-tip & Residuals. If you click on the Tree tab you will see the tree as loaded from the tree file. Because we constructed this tree using a non-molecular-clock model, it will be arbitrarily rooted. If you look at the date of each virus in the tree you will see that there is no correlation with the horizontal position:
Now switch to the Root-to-tip panel. This shows a plot of the divergence from the root of the tree against time of sampling (a so-called ‘Root to tip plot’):
You can see that there is very little correlation in this plot (the line is the best-fit regression). In the table on the left you can see the Correlation Coefficient is 0.35. This lack of correlation is expected as the root is arbitrarily set by the phylogeny reconstruction software and thus divergence from root is meaningless. TempEst can try to find the root of the tree that optimizes the temporal signal. It does this by trying all possible roots and picks the one that produces the optimal value of a range of statistics. The function it uses is selected in the menu at the top left. The options are to minimize the mean of the squares of the residuals (residual-mean-squared), or to maximize the correlation coefficient (correlation) or R2 (R squared). These are all ad hoc procedures and no particular one is best but residual-mean-squared may be most consistent with the investigations here.
Click Best-fitting root to root the tree at the place that minimizes the mean of the squares of the residuals.
Now there is a better correlation between the dates of the tips and the divergence from the root (the correlation coefficient has nearly doubled). Return to the tree to look where the root was placed:
To make the tree easier to view, switch the Order option in the panel at the bottom to increasing. This rotates each node so the branch with the most tips is at the top. You can see now that there are 3 main lineages in this influenza tree - the human lineage at the top starting with the BrevigMission virus from 1918, the swine lineage in the middle and the avian lineage at the bottom.
The tree branches are coloured to show the residual with blue for tips with positive residuals (above the regression line), red for negative.
On the left hand side of the window there is a table of statistics:
As well as the statistical metrics (Correlation Coefficient, R squared and Residual Mean Squared) there are the following:Date rangeThe span of dates for the viruses.Slope (rate)The slope of the regression line. This is an estimate of the rate of evolution in substitutions per site per year.X-Intercept (TMRCA)The point on the x-axis at which the regression line crosses. This is an estimate of the date of the root of the tree.Finding and interpreting problematic sequences
Switch to the Root-to-tip panel. Look for the point furthest from the line in the top left hand quadrant. If you click and drag your pointer over the point it will be highlighted in a blue colour:
If you now switch to the Residual panel you will see a plot of all the residuals (the tangental deviation from the regression line). The virus we selected will still be highlighted and you can see it is an outlier. It is often easiest to select outliers in this plot.
If we now go back to the Tree panel you will see the label of the selected virus hilighted. You can use the Zoom slider in the bottom panel to zoom in on the area of the tree and the Font Size selector to increase the size of the label:
Looking at this part of the tree you should be able to see why A.BrantGoose.1.1917 is such an outlier. Although it is supposedly sampled from 1917, it is actually identical to a bunch of 4 other bird viruses from Ohio in 1999. This suggests that this virus sequence was the result of contamination by one of the other viruses in the same lab (another possibility is the mis-labelling of samples).
Adobe Photoshop Crack with torrent Win/Mac (32bit+64bit) Adobe Photoshop Crack 2020 can be an entire method for professionals digital imaging that features a fantastic concept to execute new intuitive tools for creating images, pictures, three-dimensional projects. Adobe photoshop CC 2020 crack is part of this creative cloud which gets got the capability to provide the users with the latest. Adobe Photoshop 2020 Crack v21.2.1.265 Mac Torrent Download. July 8, 2020, Thomas, No Comment. Adobe Photoshop 2020 Crack v21.2.1.265 Torrent Full Version Latest I want to send you a new version of Adobe Photoshop 2020 Crack for Mac with a serial number, which is part of Creative Cloud. Adobe photoshop for mac torrent with crack. Adobe Photoshop 2020 Crack v21.2.1.265 Torrent Full Version Latest I want to send you a new version of Adobe Photoshop 2020 Crack for Mac with a serial number, which is part of Creative Cloud. Adobe Photoshop is one of the best graphic raster editors that can work with a large number of graphic formats.Note: The influenza virus sequence, A.BrantGoose.1.1917, was published in a paper entitled ‘1917 Avian Influenza Virus Sequences Suggest that the 1918 Pandemic Virus Did Not Acquire Its Hemagglutinin Directly from Birds’. This paper used the fact that this sequence, from prior to the 1918 human pandemic, phylogenetically grouped with viruses from ‘modern’ birds to suggest that the 1918 pandemic was not a direct cross-over from birds. Clearly this interpretation is unsupported because of the likelihood of lab contamination as a source of the virus.
One further tool is available that can be useful to find problematic sequences. Turn on the Show ancestor traces option at the bottom of the panel:
This option draws a green line from the selected virus to the point on the regression line where the immediate ancestor should lie (i.e., given its divergence from the root). If the line, like the example here, is horizontal and extends to the left, this suggests the sequence is actually more recent than the date that it has been given. This may be indicative of contamination from a recent virus than the supposed date or a mislabelling (another issue is that the date format could be wrongly parsed).
Ancestor lines that are vertical upwards suggest that the sequence has too many unique differences compared to its ancestor. This may be indicative of sequencing error, degraded samples, host restriction-factor editing, alignment issues, or recombination.
Ancestor lines that are horizontal and to the right mean that the supposed date of the virus is more recent than the divergence would suggest. This can be due to contamination by an older virus (or a mislabelling).
The ancestor lines can never be downwards as this would denote a negative divergence. Shorter ancestor lines and ones that lie close to the regression gradient are less likely to be problematic.
Go to the Residuals panel and select the most left hand (negative) residual point:
Then return to the tree and examine the selected virus:
You can see here that the selected virus, A.swine.StHyacinthe.148.1990, although supposedly from 1990, is identical to a virus from Iowa in 1930. A/swine/Iowa/15/1930 is a commonly used lab virus and thus this is likely, again, a contamination issue.Note: If the ascribed date of A.swine.StHyacinthe.148.1990 is correct, it would mean that this virus is directly descended from the 1930s viruses but hasn’t evolved at all in this time. This would require the virus to have been frozen and then re-emerge 60 years later. Although this is not entirely implausible it is unlikely to have happened in this case.
There are 4 other examples of this type of problematic sequences in this data set. See if you can identify them.Cleaning the data set
Once all of the problematic sequences have been identified, these can be removed from the alignment and the tree rebuilt to see the effect they were having onb the analysis. Download the file, ice_viruses_cleaned.fasta, which has had 7 problematic sequences removed. Download the file, ice_viruses_cleaned.fasta, here.
Using the instructions given above, for the file ice_viruses_cleaned.fasta, repeat the tree building procedure using IQ-Tree, load the resulting tree into TempEst and parse the dates for each virus. Switch to the Root-to-tip panel, turn on Best-fitting root and compare the plot to the one you got before. You should see something like this:
You can see that the correlation between divergence from root and time of sampling is much better (the Correlation Coefficent in the table on the left is now 0.733).
You will notice that the relationship is still not very clean. The reason for this is that there are 3 different lineages here (human, swine and avian) and that combining them all into a single tree (which is then fixed) may obscure their individual patterns.
The final file in this analysis, ice_viruses_human.fasta, is one that contains only the human viruses. Download the file, ice_viruses_human.fasta, here.
Repeating the steps above to build a tree and load it into TempEst now shows this relationship:
In this image everything after 1975 is highlighted in blue. What you should be able to see is that there are actually two lines of points here, one from 1918 to 1957 and one from 1977 to 2000. There is a gap in time (in the horizontal axis) of about 20 years but no gap in the divergence from the root.Note: This gap in time for the H1N1 human lineage has been well described. In the influenza pandemic of 1957-1958 an H2N2 subtype emerged which displaced the H1N1 lineage which had been circulating as seasonal flu since 1918. The H2N2 lineage became the seasonal flu until it in turn was replaced by the H3N2 subtype in 1968. Then in 1977 another pandemic occurred in which the same H1N1 lineage as had previously been circulating reemerged as a second season flu type (it then continued to circulate until 2009 when it was replaced by the ‘swine flu’ H1N1). What was remarkable about the H1N1 viruses that emerged in 1977 (as we can see in our tree) was that they were very similar to those from the 1940s and 1950s. So similar that they seemed not to have been evolving for 20 years. This was not a case of contamination as 1000s of post 1977 viruses have been sequenced. It is almost certain that the H1N1 virus that emerged in 1977 had been frozen and was the result of an escape from a lab. > > Tempest 20004.83 / 5 - 6 votesDescription of Tempest 2000Read Full Description
Back in the early 1980s, Atari’s Tempest was one of the best-selling games on both home systems and in the arcades.
Given the current prettier-means-better thinking in the computer games industry, it’s no small wonder that Tempest 2000 has not followed the overly ambitious, let’s-make-the-game-in-3D trend of some other recent video-game comebacks. Instead, Tempest 2000 tries to preserve the addictive fun while upping the ’kinetic ante’ of the original. In other words, it tries to compound on the original Tempest’s specialty, which is fast-paced, in-your-face noise and action. To that end, Tempest 2000 succeeds-perhaps far too well.
As in the original the game allows players to manipulate a 3-D vortex while avoiding missiles and spikes. There are 3-D enemies, awesome weapons and many visual effects. The game is much, much harder than the 1980s original: webs don’t just sit on the screen while you travel around them- they bob up and down and around, which sometimes means that one side of the web or the other is not always visible on the screen. All the original enemies in Tempest are here, plus you now get Mutant Flippers, Demon Heads, and UFO’s, all much more aggressive and more elusive than the old enemies.
To complicate things, ’power-ups’ are now sometimes fired at you, and if you catch them, you can get extra points, extra guys, laser beams (which emit a cool noisy effect), and the power to jump in the air and fire down on your enemies. You can even get an AI-controlled robot buddy that will help you in your kill-everything cause.
Tempest was already fast-paced, but it’s arguable that Tempest 2000 is just overly frantic. The game is definitely a much more difficult, noisier version of the original. I did get addicted all over again, though, what with the jumping, laser beams, and AI robots that greatly enhance gameplay And, in the end, Tempest 2000 is similar enough in gameplay to the original that it brings back a huge dose of nostalgia. You can even blast your friends in ’Duel Mode,’ or team up in a ’Team-Up Mode.’
Both die-hard fans of the original Tempest and newcomers will have much to like in this souped-up version of the arcade hit, although they should be prepared for some serious thumb-blistering sessions. Two thumbs up!
Review By HOTUDCaptures and Snapshots
Screenshots from MobyGames.comComments and reviews
Raul2018-04-270 point DOS version
The FM music is pretty cool!
moonbug2015-03-281 point Mac version
Well there’s also a DOS version of this game. But I still prefer the original Tempest game that I played the hell out of on my Amstrad CPC. I don’t think these
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For this tutorial, the Mac OS X version will be shown but the Linux & Windows versions will have exactly the same layout and functionality. When started, TempEst will immediately display a file selection dialog box in which you can select the tree that you made in the previous section. Select iceviruses.fasta.treefile and click Open. When we created Tempest, we focused on the most thrilling part of pirate life – sea battles. As you navigate the dangerous waters of the game you won’t just catch up with merchants, but you will encounter fellow pirates, creepy followers of a mysterious cult and terrible mythical monsters: Kraken, Leviathan and other infamous creatures. Tempest is a Pirate Open World Action RPG where you rove the seas across three continents filled with dozens of colonies and forts, hundreds of quests and countless ships to plunder. Customize your ship, trade, challenge fellow pirates and face terrible mythical monsters such as Kraken and Leviathan. The Tempest KIRIN. Named after a mythological beast from East Asian folklore known for its swiftness and grace, Tempest wants to invoke a feeling of speed and fluidity whenever you use this keyboard. Ultra Durable Shine Resistant PBT Keycaps. Give us a call at (682)477-4220 to reserve your spot in class! Please make sure you fill out a waiver here first for the location you are interested in.
*Tempest For Clarinet
*Tempest Form A And B
*Tempest For Mac Wallpaper
*Tempest For Mac
*Tempest Form A Instruction GuideThis tutorial describes the use of TempEst to examine the temporal signal of a data set and to look for problematic or erroneous sequences.
In this tutorial, we will explore the use of the interactive graphical program TempEst (formerly known as Path-O-Gen) to examine virus sequence data that has been sampled through time to look for problematic sequences and to explore the degree and pattern of temporal signal. This can be a useful way of examining the data for potential issues before committing significant time to running BEAST.Building a non-molecular clock tree
To examine the relationship between genetic divergence and time (temporal signal), we require a phylogenetic tree constructed without assuming a molecular clock. There is a wide range of suitable software packages (i.e., PhyML, RAxML, GARLI) but for this tutorial we are going to use IQ-Tree which uses a fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood.The data for this tutorial was compiled for this paper: Worobey (2009) Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus. Journal of Virology, 82, 3769–3774. DOI: 10.1128/JVI.02207-07. This was a response to an earlier paper (Zhang et al (2006) J Virol80, 12229–12235 DOI: 10.1128/JVI.00986-06 ) which claimed to have isolated and sequenced influenza viruses from glacial ice.
You can download the file, ice_viruses.fasta, here.
Install IQ-Tree using the instructions on the website and open a command-line prompt, navigating to the directory containing the data file ice_viruses.fasta.
To build a maximum likelihood phylogenetic tree using the GTR+gamma model type:
This will create a set of files in the directory containing various outputs and results:
Join 25 million people and teams who organize, plan, and collaborate on tasks and projects with Any.do. “Best to-do list app” by the WSJ. The best calendar app for life & work. Control your day, week and month with calendar events and tasks in a single view. It’s the best way to manage your time and achieve your ambitious goals. Anydo for macbook air.
For our purposes we only need the maximum likelihood tree file ice_viruses.fasta.treefile. You can delete the other files if you like.Running TempEst and loading the treeRun TempEst by double clicking on its icon. TempEst is an interactive graphical application for examining the temporal signal in a tree of time-stamped sequences by plotting the divergence of each tip from the root against the date of sampling (a root-to-tip plot).
Once running, TempEst will look similar irrespective of which computer system it is running on. For this tutorial, the Mac OS X version will be shown but the Linux & Windows versions will have exactly the same layout and functionality.
When started, TempEst will immediately display a file selection dialog box in which you can select the tree that you made in the previous section.
Select ice_viruses.fasta.treefile and click Open.Parsing dates of sampling
Once the tree is loaded the main window will appear and look like this:
Ignore the panel on the left for the moment. The first thing that needs doing is to give the date of sampling to each of the sequences.
The actual year of sampling is given at the end of the name of each taxon. To specify the dates of the sequences in BEAUti we will use the Parse Dates button at the top of the panel. Clicking this will make a dialog box appear:Tempest For Clarinet
This operation attempts to extract the dates from the taxon names. It works by trying to find a numerical field within each name. This dialog box is the same as that in BEAUti and there are a wide range of options for doing this - See this page for details about the various options for setting dates in this panel. For these sequences you can set the options to look like the figure above: Defined just by its order, Order: last and Parse as a number option.
When parsing a number, you can ask BEAUti to add a fixed value to each date which can be useful for transforming a 2 digit year into a 4 digit year. Because all dates are specified in a four digit format in this case, no additional settings are needed. So, we can press OK.
The table will now have the year of sampling for each virus in the Dates column. Click on the Dates column header to sort the dates and check that they are all correct.The temporal signal and rooting
We can now explore the data using the tabs at the top of the window - Tree, Root-to-tip & Residuals. If you click on the Tree tab you will see the tree as loaded from the tree file. Because we constructed this tree using a non-molecular-clock model, it will be arbitrarily rooted. If you look at the date of each virus in the tree you will see that there is no correlation with the horizontal position:
Now switch to the Root-to-tip panel. This shows a plot of the divergence from the root of the tree against time of sampling (a so-called ‘Root to tip plot’):
You can see that there is very little correlation in this plot (the line is the best-fit regression). In the table on the left you can see the Correlation Coefficient is 0.35. This lack of correlation is expected as the root is arbitrarily set by the phylogeny reconstruction software and thus divergence from root is meaningless. TempEst can try to find the root of the tree that optimizes the temporal signal. It does this by trying all possible roots and picks the one that produces the optimal value of a range of statistics. The function it uses is selected in the menu at the top left. The options are to minimize the mean of the squares of the residuals (residual-mean-squared), or to maximize the correlation coefficient (correlation) or R2 (R squared). These are all ad hoc procedures and no particular one is best but residual-mean-squared may be most consistent with the investigations here.
Click Best-fitting root to root the tree at the place that minimizes the mean of the squares of the residuals.
Now there is a better correlation between the dates of the tips and the divergence from the root (the correlation coefficient has nearly doubled). Return to the tree to look where the root was placed:
To make the tree easier to view, switch the Order option in the panel at the bottom to increasing. This rotates each node so the branch with the most tips is at the top. You can see now that there are 3 main lineages in this influenza tree - the human lineage at the top starting with the BrevigMission virus from 1918, the swine lineage in the middle and the avian lineage at the bottom.
The tree branches are coloured to show the residual with blue for tips with positive residuals (above the regression line), red for negative.
On the left hand side of the window there is a table of statistics:
As well as the statistical metrics (Correlation Coefficient, R squared and Residual Mean Squared) there are the following:Date rangeThe span of dates for the viruses.Slope (rate)The slope of the regression line. This is an estimate of the rate of evolution in substitutions per site per year.X-Intercept (TMRCA)The point on the x-axis at which the regression line crosses. This is an estimate of the date of the root of the tree.Finding and interpreting problematic sequences
Switch to the Root-to-tip panel. Look for the point furthest from the line in the top left hand quadrant. If you click and drag your pointer over the point it will be highlighted in a blue colour:
If you now switch to the Residual panel you will see a plot of all the residuals (the tangental deviation from the regression line). The virus we selected will still be highlighted and you can see it is an outlier. It is often easiest to select outliers in this plot.
If we now go back to the Tree panel you will see the label of the selected virus hilighted. You can use the Zoom slider in the bottom panel to zoom in on the area of the tree and the Font Size selector to increase the size of the label:
Looking at this part of the tree you should be able to see why A.BrantGoose.1.1917 is such an outlier. Although it is supposedly sampled from 1917, it is actually identical to a bunch of 4 other bird viruses from Ohio in 1999. This suggests that this virus sequence was the result of contamination by one of the other viruses in the same lab (another possibility is the mis-labelling of samples).
Adobe Photoshop Crack with torrent Win/Mac (32bit+64bit) Adobe Photoshop Crack 2020 can be an entire method for professionals digital imaging that features a fantastic concept to execute new intuitive tools for creating images, pictures, three-dimensional projects. Adobe photoshop CC 2020 crack is part of this creative cloud which gets got the capability to provide the users with the latest. Adobe Photoshop 2020 Crack v21.2.1.265 Mac Torrent Download. July 8, 2020, Thomas, No Comment. Adobe Photoshop 2020 Crack v21.2.1.265 Torrent Full Version Latest I want to send you a new version of Adobe Photoshop 2020 Crack for Mac with a serial number, which is part of Creative Cloud. Adobe photoshop for mac torrent with crack. Adobe Photoshop 2020 Crack v21.2.1.265 Torrent Full Version Latest I want to send you a new version of Adobe Photoshop 2020 Crack for Mac with a serial number, which is part of Creative Cloud. Adobe Photoshop is one of the best graphic raster editors that can work with a large number of graphic formats.Note: The influenza virus sequence, A.BrantGoose.1.1917, was published in a paper entitled ‘1917 Avian Influenza Virus Sequences Suggest that the 1918 Pandemic Virus Did Not Acquire Its Hemagglutinin Directly from Birds’. This paper used the fact that this sequence, from prior to the 1918 human pandemic, phylogenetically grouped with viruses from ‘modern’ birds to suggest that the 1918 pandemic was not a direct cross-over from birds. Clearly this interpretation is unsupported because of the likelihood of lab contamination as a source of the virus.
One further tool is available that can be useful to find problematic sequences. Turn on the Show ancestor traces option at the bottom of the panel:
This option draws a green line from the selected virus to the point on the regression line where the immediate ancestor should lie (i.e., given its divergence from the root). If the line, like the example here, is horizontal and extends to the left, this suggests the sequence is actually more recent than the date that it has been given. This may be indicative of contamination from a recent virus than the supposed date or a mislabelling (another issue is that the date format could be wrongly parsed).
Ancestor lines that are vertical upwards suggest that the sequence has too many unique differences compared to its ancestor. This may be indicative of sequencing error, degraded samples, host restriction-factor editing, alignment issues, or recombination.
Ancestor lines that are horizontal and to the right mean that the supposed date of the virus is more recent than the divergence would suggest. This can be due to contamination by an older virus (or a mislabelling).
The ancestor lines can never be downwards as this would denote a negative divergence. Shorter ancestor lines and ones that lie close to the regression gradient are less likely to be problematic.
Go to the Residuals panel and select the most left hand (negative) residual point:
Then return to the tree and examine the selected virus:
You can see here that the selected virus, A.swine.StHyacinthe.148.1990, although supposedly from 1990, is identical to a virus from Iowa in 1930. A/swine/Iowa/15/1930 is a commonly used lab virus and thus this is likely, again, a contamination issue.Note: If the ascribed date of A.swine.StHyacinthe.148.1990 is correct, it would mean that this virus is directly descended from the 1930s viruses but hasn’t evolved at all in this time. This would require the virus to have been frozen and then re-emerge 60 years later. Although this is not entirely implausible it is unlikely to have happened in this case.
There are 4 other examples of this type of problematic sequences in this data set. See if you can identify them.Cleaning the data set
Once all of the problematic sequences have been identified, these can be removed from the alignment and the tree rebuilt to see the effect they were having onb the analysis. Download the file, ice_viruses_cleaned.fasta, which has had 7 problematic sequences removed. Download the file, ice_viruses_cleaned.fasta, here.
Using the instructions given above, for the file ice_viruses_cleaned.fasta, repeat the tree building procedure using IQ-Tree, load the resulting tree into TempEst and parse the dates for each virus. Switch to the Root-to-tip panel, turn on Best-fitting root and compare the plot to the one you got before. You should see something like this:
You can see that the correlation between divergence from root and time of sampling is much better (the Correlation Coefficent in the table on the left is now 0.733).
You will notice that the relationship is still not very clean. The reason for this is that there are 3 different lineages here (human, swine and avian) and that combining them all into a single tree (which is then fixed) may obscure their individual patterns.
The final file in this analysis, ice_viruses_human.fasta, is one that contains only the human viruses. Download the file, ice_viruses_human.fasta, here.
Repeating the steps above to build a tree and load it into TempEst now shows this relationship:
In this image everything after 1975 is highlighted in blue. What you should be able to see is that there are actually two lines of points here, one from 1918 to 1957 and one from 1977 to 2000. There is a gap in time (in the horizontal axis) of about 20 years but no gap in the divergence from the root.Note: This gap in time for the H1N1 human lineage has been well described. In the influenza pandemic of 1957-1958 an H2N2 subtype emerged which displaced the H1N1 lineage which had been circulating as seasonal flu since 1918. The H2N2 lineage became the seasonal flu until it in turn was replaced by the H3N2 subtype in 1968. Then in 1977 another pandemic occurred in which the same H1N1 lineage as had previously been circulating reemerged as a second season flu type (it then continued to circulate until 2009 when it was replaced by the ‘swine flu’ H1N1). What was remarkable about the H1N1 viruses that emerged in 1977 (as we can see in our tree) was that they were very similar to those from the 1940s and 1950s. So similar that they seemed not to have been evolving for 20 years. This was not a case of contamination as 1000s of post 1977 viruses have been sequenced. It is almost certain that the H1N1 virus that emerged in 1977 had been frozen and was the result of an escape from a lab. > > Tempest 20004.83 / 5 - 6 votesDescription of Tempest 2000Read Full Description
Back in the early 1980s, Atari’s Tempest was one of the best-selling games on both home systems and in the arcades.
Given the current prettier-means-better thinking in the computer games industry, it’s no small wonder that Tempest 2000 has not followed the overly ambitious, let’s-make-the-game-in-3D trend of some other recent video-game comebacks. Instead, Tempest 2000 tries to preserve the addictive fun while upping the ’kinetic ante’ of the original. In other words, it tries to compound on the original Tempest’s specialty, which is fast-paced, in-your-face noise and action. To that end, Tempest 2000 succeeds-perhaps far too well.
As in the original the game allows players to manipulate a 3-D vortex while avoiding missiles and spikes. There are 3-D enemies, awesome weapons and many visual effects. The game is much, much harder than the 1980s original: webs don’t just sit on the screen while you travel around them- they bob up and down and around, which sometimes means that one side of the web or the other is not always visible on the screen. All the original enemies in Tempest are here, plus you now get Mutant Flippers, Demon Heads, and UFO’s, all much more aggressive and more elusive than the old enemies.
To complicate things, ’power-ups’ are now sometimes fired at you, and if you catch them, you can get extra points, extra guys, laser beams (which emit a cool noisy effect), and the power to jump in the air and fire down on your enemies. You can even get an AI-controlled robot buddy that will help you in your kill-everything cause.
Tempest was already fast-paced, but it’s arguable that Tempest 2000 is just overly frantic. The game is definitely a much more difficult, noisier version of the original. I did get addicted all over again, though, what with the jumping, laser beams, and AI robots that greatly enhance gameplay And, in the end, Tempest 2000 is similar enough in gameplay to the original that it brings back a huge dose of nostalgia. You can even blast your friends in ’Duel Mode,’ or team up in a ’Team-Up Mode.’
Both die-hard fans of the original Tempest and newcomers will have much to like in this souped-up version of the arcade hit, although they should be prepared for some serious thumb-blistering sessions. Two thumbs up!
Review By HOTUDCaptures and Snapshots
Screenshots from MobyGames.comComments and reviews
Raul2018-04-270 point DOS version
The FM music is pretty cool!
moonbug2015-03-281 point Mac version
Well there’s also a DOS version of this game. But I still prefer the original Tempest game that I played the hell out of on my Amstrad CPC. I don’t think these
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